Invalid argument: --no-solvation Usage: /nfs/home/rstein/zzz.github/DOCK/ligand/generate/build_database_ligand.sh [OPTIONS] Options: -h, --help - Display this message and exit -H, --pH - A quoted, space separated list of pH levels to build tautomers/protomers at -s, --single - Build a single db/db2 file instead of separate files for each protomer -n, --name - Override database name -d, --dir - Working directory -c, --covalent - Build a covalent library instead of standard -3, --3d - Use provided 3D structures (implies --pre-tautomerized) --no-limit-confs-by-hydrogens - Don't limit # conformations by # rotatable hydrogens --pre-tautomerized - Treat input file as pre-generated tautomers --permissive-taut-prot - Use lower tautomer and protomer cutoffs --no-conformations - Skip generating multiple rigid fragment conformations --no-db - Skip building db files --no-db2 - Skip building db2 files --no-solvation - Don't save solvation files --no-mol2 - Don't save mol2 files --save-table - Save the full protomer table --bad-charges - List of bad protonation patterns to exclude --debug - Extra debugging output Overrideable Sub-programs: TAUOMERIZE_PROTONATE_EXE - Generate (multiple) tautomerized and protonated variants of the input substances at a pH level PROTOMER_COALESE_EXE - Filter and merge protomers over pH levels PROTOMER_STEREOCENTERS_EXE - Expand any new stereocenters from protonation EMBED_PROTOMERS_3D_EXE - Create 3D mol2 files for each protomer (names should JUST be the line number of the protomer without any extension) PREPARE_NAME_EXE - Write the name.txt file to build a db2 file with SOLVATION_EXE - Calculation solvation for a given mol2 file GENERATE_CONFORMATIONS_EXE - Generate heirarchy conformations GENERATE_RIGID_FRAGMENT_CONFORMATIONS_EXE - Generate standard heirarchy conformations GENERATE_COVALENT_CONFORMATIONS_EXE - Generate covalent heirarchy conformations BUILD_DB2_EXE - Generate a db2 file from conformations BUILD_DB_EXE - Genearte a db file from conformations STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/stefan/7898178/working' mkdir: created directory `/scratch/stefan/7898178/working/protonate' Storing results in /scratch/stefan/7898178/finished Working in /scratch/stefan/7898178/working /scratch/stefan/7898178/working /scratch/stefan/7898178 /scratch/stefan/7898178/working/protonate /scratch/stefan/7898178/working /scratch/stefan/7898178 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 297 protomers created Coalesing and merging protomers 293 protomers generated for 143 compounds Checking for new stereocenters and expanding 294 protomers after new stereo-center expansion /scratch/stefan/7898178/working /scratch/stefan/7898178 Bulk generating 3D conformations all protomers in /scratch/stefan/7898178/working/3D mkdir: created directory `/scratch/stefan/7898178/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7898178/working/protonate/xaaaafj_worked-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' 295 3D conformations generated for 143 compounds Building REAL300019758202 mkdir: created directory `/scratch/stefan/7898178/working/building' mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758202' /scratch/stefan/7898178/working/building/REAL300019758202 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758202 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758202/0 /scratch/stefan/7898178/working/building/REAL300019758202 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/1 `/scratch/stefan/7898178/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=N[N-]N=N1) `REAL300019758202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758202 none CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 149, 91, 32, 90, 6, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 168, 168, 168, 168, 149, 149, 91, 91, 91, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 725 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758202 none CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 8, 8, 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, 7, 7, 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: [8, 1, 8, 15, 19, 19, 25, 25, 31, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 19, 19, 19, 31, 31, 43, 43, 43] 43 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758202 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758202/1 /scratch/stefan/7898178/working/building/REAL300019758202 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/2 `/scratch/stefan/7898178/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=NN=N[N-]1) `REAL300019758202.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758202 none CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 147, 90, 32, 89, 6, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 168, 168, 168, 168, 147, 147, 90, 90, 90, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 732 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758202 none CC(CN(C)C(=O)CC1=CC=C(F)C(Cl)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 8, 8, 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, 7, 7, 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: [8, 1, 8, 15, 19, 19, 25, 25, 31, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 19, 19, 19, 31, 31, 43, 43, 43] 43 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758202 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758202 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `/scratch/stefan/7898178/finished' Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758202/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758202/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758202 Building REAL300019758203 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758203' /scratch/stefan/7898178/working/building/REAL300019758203 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758203 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758203/0 /scratch/stefan/7898178/working/building/REAL300019758203 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/3 `/scratch/stefan/7898178/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1) `REAL300019758203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 3, 4, 1, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [37, 38, 7, 8, 14, 15, 16, 17, 5] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 3, 4, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 25 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 23 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758203 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758203/1 /scratch/stefan/7898178/working/building/REAL300019758203 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/4 `/scratch/stefan/7898178/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1) `REAL300019758203.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 3, 4, 1, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [37, 38, 7, 8, 14, 15, 16, 17, 5] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 3, 4, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 25 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758203 none CC(CN(C)C(=O)C1(C2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 23 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758203 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758203 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758203/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758203/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758203 Building REAL300019758204 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758204' /scratch/stefan/7898178/working/building/REAL300019758204 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758204 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758204/0 /scratch/stefan/7898178/working/building/REAL300019758204 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/5 `/scratch/stefan/7898178/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=N[N-]N=N1) `REAL300019758204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758204 none CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 152, 110, 63, 110, 29, 63, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 159, 159, 159, 159, 152, 152, 111, 111, 111, 29, 29, 14, 14, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 717 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758204 none CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 48, 48, 85, 85, 97, 107, 148, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 48, 48, 48, 97, 97, 107, 107, 201, 201, 201] 201 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38]) total number of confs: 598 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758204 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758204/1 /scratch/stefan/7898178/working/building/REAL300019758204 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/6 `/scratch/stefan/7898178/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=NN=N[N-]1) `REAL300019758204.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758204 none CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 154, 108, 63, 108, 29, 63, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 201, 161, 161, 161, 161, 154, 154, 109, 109, 109, 29, 29, 14, 14, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 733 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758204 none CC(CN(C)C(=O)CCOC1=CC=C(Cl)C(F)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 49, 49, 86, 86, 97, 107, 148, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 49, 49, 49, 97, 97, 107, 107, 201, 201, 201] 201 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38]) total number of confs: 594 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758204 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758204 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758204/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758204/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758204 Building REAL300019758205 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758205' /scratch/stefan/7898178/working/building/REAL300019758205 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758205 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758205/0 /scratch/stefan/7898178/working/building/REAL300019758205 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/7 `/scratch/stefan/7898178/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=N[N-]N=N1) `REAL300019758205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758205 none CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [72, 57, 24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 72, 88, 88, 88, 88, 72, 72, 72, 72, 57, 57, 24, 24, 24, 1, 1] 88 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 331 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758205 none CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 26, 39, 39, 74, 74, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 39, 39, 39, 88, 88] 88 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 284 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758205 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758205/1 /scratch/stefan/7898178/working/building/REAL300019758205 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/8 `/scratch/stefan/7898178/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=NN=N[N-]1) `REAL300019758205.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758205 none CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [72, 57, 24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 72, 88, 88, 88, 88, 72, 72, 72, 72, 57, 57, 24, 24, 24, 1, 1] 88 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 331 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758205 none CC(CN(C)C(=O)C1=CSC=C1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 25, 38, 38, 71, 71, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 38, 38, 38, 87, 87] 87 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 280 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758205 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758205 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758205/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758205/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758205 Building REAL300019758206 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758206' /scratch/stefan/7898178/working/building/REAL300019758206 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758206 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758206/0 /scratch/stefan/7898178/working/building/REAL300019758206 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/9 `/scratch/stefan/7898178/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)N(C)CC(C)C1=N[N-]N=N1)C1=CC=C(Cl)C=C1) `REAL300019758206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758206 none CCCC(C(=O)N(C)CC(C)C1=N[N-]N=N1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 16, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 6, 6, 6, 6, 16, 16, 16, 16] 16 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758206 none CCCC(C(=O)N(C)CC(C)C1=N[N-]N=N1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 3, 5, 5, 10, 11, 11, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 10, 10, 11, 11, 11, 11, 1, 1, 1, 1] 16 rigid atoms, others: [3, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758206 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758206/1 /scratch/stefan/7898178/working/building/REAL300019758206 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/10 `/scratch/stefan/7898178/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)N(C)CC(C)C1=NN=N[N-]1)C1=CC=C(Cl)C=C1) `REAL300019758206.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758206 none CCCC(C(=O)N(C)CC(C)C1=NN=N[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 12, 16, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 6, 6, 6, 6, 16, 16, 16, 16] 16 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758206 none CCCC(C(=O)N(C)CC(C)C1=NN=N[N-]1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 3, 3, 3, 5, 5, 10, 11, 11, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 10, 10, 11, 11, 11, 11, 1, 1, 1, 1] 16 rigid atoms, others: [3, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758206 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758206 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758206/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758206/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758206 Building REAL300019758207 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758207' /scratch/stefan/7898178/working/building/REAL300019758207 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758207 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758207/0 /scratch/stefan/7898178/working/building/REAL300019758207 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/11 `/scratch/stefan/7898178/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 16, 15, 27, 43, 43, 56, 56, 56, 56, 2, 2, 2, 3, 3, 3, 3, 4, 3, 4, 3, 3, 2, 2, 2, 16, 16, 16, 27, 26, 43, 43, 43, 43] 61 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 3, 3, 18, 18, 39, 40, 56, 61, 61, 61, 61, 61, 61, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 40, 40, 40, 57, 57, 61, 61, 61, 61] 61 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 61, 61, 61, 61, 61, 56, 56, 41, 26, 41, 17, 26, 9, 1, 9, 1, 1, 1, 1, 1, 56, 56, 56, 61, 61, 61, 61, 61, 61, 61, 61, 61, 56, 56, 56, 26, 26, 26, 17, 17, 9, 9, 9, 9] 61 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758207 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758207/1 /scratch/stefan/7898178/working/building/REAL300019758207 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/12 `/scratch/stefan/7898178/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758207.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 16, 15, 27, 43, 43, 56, 56, 56, 56, 2, 2, 2, 3, 3, 3, 3, 4, 3, 4, 3, 3, 2, 2, 2, 16, 16, 16, 27, 26, 43, 43, 43, 43] 61 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 3, 3, 18, 18, 39, 40, 56, 61, 61, 61, 61, 61, 61, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 40, 40, 40, 57, 57, 61, 61, 61, 61] 61 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758207 none CC1=NN(C2CCOCC2)C(C)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 61, 61, 61, 61, 61, 56, 56, 41, 26, 41, 17, 26, 9, 1, 9, 1, 1, 1, 1, 1, 56, 56, 56, 61, 61, 61, 61, 61, 61, 61, 61, 61, 56, 56, 56, 26, 26, 26, 17, 17, 9, 9, 9, 9] 61 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758207 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758207 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758207/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758207/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758207 Building REAL300019758208 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758208' /scratch/stefan/7898178/working/building/REAL300019758208 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758208 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758208/0 /scratch/stefan/7898178/working/building/REAL300019758208 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/13 `/scratch/stefan/7898178/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758208 none CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [10, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 10, 10, 18, 18, 25, 26, 26, 28, 28, 28, 28, 10, 10, 10, 10, 10, 8, 4, 1, 1, 1, 18, 18, 18, 25, 25, 26, 26, 26, 26] 28 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758208 none CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [27, 22, 19, 22, 27, 28, 28, 28, 28, 28, 28, 16, 19, 13, 16, 6, 1, 6, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 22, 27, 28, 28, 28, 16, 16, 16, 13, 13, 6, 6, 6, 6] 28 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758208 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758208/1 /scratch/stefan/7898178/working/building/REAL300019758208 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/14 `/scratch/stefan/7898178/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758208.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758208 none CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [10, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 10, 10, 18, 18, 25, 26, 26, 28, 28, 28, 28, 10, 10, 10, 10, 10, 8, 4, 1, 1, 1, 18, 18, 18, 25, 25, 26, 26, 26, 26] 28 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758208 none CCC(NC1=CC=CN=C1Cl)C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 16, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [27, 22, 19, 22, 27, 28, 28, 28, 28, 28, 28, 16, 19, 13, 16, 6, 1, 6, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 22, 27, 28, 28, 28, 16, 16, 16, 13, 13, 6, 6, 6, 6] 28 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758208 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758208 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758208/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758208/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758208 Building REAL300019758209 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758209' /scratch/stefan/7898178/working/building/REAL300019758209 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758209 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758209/0 /scratch/stefan/7898178/working/building/REAL300019758209 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/15 `/scratch/stefan/7898178/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=N[N-]N=N1) `REAL300019758209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758209 none CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 31, 17, 5, 17, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 47, 47, 47, 47, 40, 40, 40, 40, 31, 31, 17, 17, 17, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 177 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758209 none CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 19, 28, 28, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 28, 28, 28, 48, 48, 48, 48, 48, 48] 48 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37]) total number of confs: 168 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758209 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758209/1 /scratch/stefan/7898178/working/building/REAL300019758209 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/16 `/scratch/stefan/7898178/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=NN=N[N-]1) `REAL300019758209.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758209 none CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 32, 17, 5, 17, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 48, 48, 48, 48, 41, 41, 41, 41, 32, 32, 17, 17, 17, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758209 none CC(CN(C)C(=O)C1CS(=O)(=O)CC1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 5, 14, 11, 11, 5, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 19, 28, 28, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 28, 28, 28, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37]) total number of confs: 172 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758209 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758209 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758209/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758209/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758209 Building REAL300019758210 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758210' /scratch/stefan/7898178/working/building/REAL300019758210 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758210 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758210/0 /scratch/stefan/7898178/working/building/REAL300019758210 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/17 `/scratch/stefan/7898178/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=N[N-]N=N1) `REAL300019758210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758210 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 4, 2, 4, 1, 2, 1, 1, 5, 5, 9, 10, 10, 10, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 10, 9, 9, 9, 9, 7, 7, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [48, 50, 5, 51, 7, 8, 44, 45, 46, 15, 16, 17, 18, 19, 20, 53, 54, 55, 52, 49, 47] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758210 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 8, 8, 10, 10, 10, 19, 19, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 23 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758210 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758210/1 /scratch/stefan/7898178/working/building/REAL300019758210 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/18 `/scratch/stefan/7898178/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=NN=N[N-]1) `REAL300019758210.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758210 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 4, 2, 4, 1, 2, 1, 1, 5, 5, 9, 10, 10, 10, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 10, 9, 9, 9, 9, 7, 7, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [48, 50, 5, 51, 7, 8, 44, 45, 46, 15, 16, 17, 18, 19, 20, 53, 54, 55, 52, 49, 47] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758210 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)CCCCCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 8, 8, 10, 10, 10, 19, 19, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 23 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758210 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758210 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758210/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758210/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758210 Building REAL300019758211 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758211' /scratch/stefan/7898178/working/building/REAL300019758211 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758211 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758211/0 /scratch/stefan/7898178/working/building/REAL300019758211 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/19 `/scratch/stefan/7898178/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758211 none COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', '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, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 1, 1, 6, 6, 20, 20, 48, 74, 74, 123, 123, 123, 123, 4, 4, 4, 1, 1, 1, 21, 21, 21, 48, 48, 74, 74, 74, 74] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 12, 13, 28, 29, 30] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758211 none COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', '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, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 122, 122, 122, 122, 122, 122, 122, 197, 201, 201, 201, 78, 43, 78, 26, 43, 11, 1, 11, 1, 1, 1, 1, 1, 126, 136, 136, 122, 122, 122, 43, 43, 43, 26, 26, 11, 11, 11, 11] 201 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758211 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758211/1 /scratch/stefan/7898178/working/building/REAL300019758211 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/20 `/scratch/stefan/7898178/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758211.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758211 none COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', '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, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 1, 1, 6, 6, 20, 20, 48, 74, 74, 122, 122, 122, 122, 4, 4, 4, 1, 1, 1, 21, 21, 21, 48, 48, 74, 74, 74, 74] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 12, 13, 28, 29, 30] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758211 none COC1=CC=CC(OC(F)(F)F)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', '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, 12, 5, 15, 15, 15, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 123, 123, 123, 123, 123, 123, 123, 197, 201, 201, 201, 80, 44, 80, 26, 44, 11, 1, 11, 1, 1, 1, 1, 1, 128, 137, 137, 123, 123, 123, 44, 44, 44, 26, 26, 11, 11, 11, 11] 201 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 536 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758211 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758211 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758211/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758211/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758211 Building REAL300019758212 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758212' /scratch/stefan/7898178/working/building/REAL300019758212 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758212 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758212/0 /scratch/stefan/7898178/working/building/REAL300019758212 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/21 `/scratch/stefan/7898178/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=N[N-]N=N1) `REAL300019758212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [124, 90, 46, 27, 46, 12, 27, 1, 12, 12, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 124, 181, 181, 181, 181, 124, 124, 124, 124, 90, 90, 46, 46, 46, 1, 7, 7, 6, 7, 7] 181 rigid atoms, others: [35, 7, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 700 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 171, 123, 86, 123, 47, 86, 7, 47, 47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 181, 181, 181, 181, 181, 181, 181, 181, 181, 171, 171, 123, 123, 123, 7, 1, 1, 1, 1, 1] 181 rigid atoms, others: [36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 743 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 37, 37, 73, 73, 80, 80, 80, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 37, 37, 37, 123, 123, 123, 123, 123, 123] 123 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 371 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758212 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758212/1 /scratch/stefan/7898178/working/building/REAL300019758212 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/22 `/scratch/stefan/7898178/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=NN=N[N-]1) `REAL300019758212.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [123, 90, 46, 27, 46, 12, 27, 1, 12, 12, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 123, 182, 182, 182, 182, 123, 123, 123, 123, 90, 90, 46, 46, 46, 1, 7, 7, 6, 7, 7] 182 rigid atoms, others: [35, 7, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 696 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 172, 125, 89, 125, 49, 89, 7, 49, 49, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 182, 182, 182, 182, 182, 182, 182, 182, 182, 172, 172, 125, 125, 125, 7, 1, 1, 1, 1, 1] 182 rigid atoms, others: [36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 735 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758212 none CC(CN(C)C(=O)C(F)(F)N1C=C(C2=CC=CC=C2)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 37, 37, 74, 74, 81, 81, 81, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 37, 37, 37, 123, 123, 123, 123, 123, 123] 123 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 371 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758212 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758212 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758212/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758212/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758212 Building REAL300019758213 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758213' /scratch/stefan/7898178/working/building/REAL300019758213 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758213 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758213/0 /scratch/stefan/7898178/working/building/REAL300019758213 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/23 `/scratch/stefan/7898178/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1) `REAL300019758213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758213 none COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 11, 6, 13, 13, 15, 15, 22, 26, 26, 31, 31, 31, 31, 1, 3, 3, 3, 1, 1, 1, 6, 11, 11, 11, 15, 15, 15, 22, 22, 26, 26, 26, 26, 1] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 22, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758213 none COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 30, 30, 30, 30, 30, 21, 15, 21, 24, 13, 15, 10, 13, 8, 1, 8, 1, 1, 1, 1, 1, 30, 34, 34, 34, 30, 30, 30, 21, 24, 24, 24, 13, 13, 13, 10, 10, 8, 8, 8, 8, 30] 34 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758213 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758213/1 /scratch/stefan/7898178/working/building/REAL300019758213 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/24 `/scratch/stefan/7898178/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1) `REAL300019758213.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758213 none COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 11, 6, 13, 13, 15, 15, 22, 26, 26, 31, 31, 31, 31, 1, 3, 3, 3, 1, 1, 1, 6, 11, 11, 11, 15, 15, 15, 22, 22, 26, 26, 26, 26, 1] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 22, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758213 none COC1=CC=CC(C(OC)C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 30, 30, 30, 30, 30, 20, 14, 20, 23, 12, 14, 9, 12, 7, 1, 7, 1, 1, 1, 1, 1, 30, 34, 34, 34, 30, 30, 30, 20, 23, 23, 23, 12, 12, 12, 9, 9, 7, 7, 7, 7, 30] 34 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758213 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758213 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758213/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758213/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758213 Building REAL300019758214 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758214' /scratch/stefan/7898178/working/building/REAL300019758214 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758214 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758214/0 /scratch/stefan/7898178/working/building/REAL300019758214 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/25 `/scratch/stefan/7898178/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCOCCCC(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758214 none COCCOCCOCCCC(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 20, 20, 11, 11, 11, 11, 10, 9, 10, 8, 9, 6, 1, 6, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 9, 9, 9, 8, 8, 6, 7, 7, 7] 21 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758214 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758214/1 /scratch/stefan/7898178/working/building/REAL300019758214 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/26 `/scratch/stefan/7898178/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCOCCCC(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758214.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758214 none COCCOCCOCCCC(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 12, 10, 12, 9, 10, 7, 1, 7, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 14, 14, 10, 10, 10, 9, 9, 6, 7, 7, 7] 21 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758214 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758214 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758214/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758214/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758214 Building REAL300019758215 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758215' /scratch/stefan/7898178/working/building/REAL300019758215 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758215 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758215/0 /scratch/stefan/7898178/working/building/REAL300019758215 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/27 `/scratch/stefan/7898178/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2C=C1OC) `REAL300019758215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758215 none COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28, 68, 114, 114, 136, 136, 136, 136, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 28, 28, 28, 68, 68, 114, 114, 114, 114, 1, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 20, 21, 22, 23, 24, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 554 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758215 none COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 43, 43, 43, 43, 43, 43, 27, 24, 27, 21, 24, 12, 1, 12, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 69, 69, 69, 69, 43, 43, 43, 24, 24, 24, 21, 21, 12, 12, 12, 12, 43, 43, 69, 69, 69] 69 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758215 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758215/1 /scratch/stefan/7898178/working/building/REAL300019758215 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/28 `/scratch/stefan/7898178/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2C=C1OC) `REAL300019758215.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758215 none COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28, 68, 113, 113, 135, 135, 135, 135, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 28, 28, 28, 68, 68, 113, 113, 113, 113, 1, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 20, 21, 22, 23, 24, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 548 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758215 none COC1=CC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 43, 43, 43, 43, 43, 43, 27, 24, 27, 20, 24, 11, 1, 11, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 69, 69, 69, 69, 43, 43, 43, 24, 24, 24, 20, 20, 11, 11, 11, 11, 43, 43, 69, 69, 69] 69 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758215 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758215 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758215/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758215/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758215 Building REAL300019758216 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758216' /scratch/stefan/7898178/working/building/REAL300019758216 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758216 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758216/0 /scratch/stefan/7898178/working/building/REAL300019758216 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/29 `/scratch/stefan/7898178/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=NN=N[N-]1) `REAL300019758216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [73, 69, 48, 26, 48, 9, 26, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 73, 83, 83, 83, 83, 73, 73, 73, 73, 69, 69, 48, 48, 48, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [43, 36, 37, 38, 7, 8, 9, 42, 39, 14, 15, 16, 17, 18, 41, 40] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [87, 84, 62, 33, 62, 19, 33, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 87, 97, 97, 97, 97, 87, 87, 87, 87, 84, 84, 62, 62, 62, 19, 19, 1, 5, 5, 5, 5, 5, 5, 5, 5] 97 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 356 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 21, 30, 30, 36, 36, 53, 77, 90, 90, 90, 90, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 30, 30, 30, 53, 53, 90, 77, 77, 77, 77, 77, 77, 77, 77] 90 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 330 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758216 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758216/1 /scratch/stefan/7898178/working/building/REAL300019758216 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/30 `/scratch/stefan/7898178/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=N[N-]N=N1) `REAL300019758216.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [73, 69, 48, 26, 48, 9, 26, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 73, 83, 83, 83, 83, 73, 73, 73, 73, 69, 69, 48, 48, 48, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [43, 36, 37, 38, 7, 8, 9, 42, 39, 14, 15, 16, 17, 18, 41, 40] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [87, 84, 62, 33, 62, 19, 33, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 87, 97, 97, 97, 97, 87, 87, 87, 87, 84, 84, 62, 62, 62, 19, 19, 1, 5, 5, 5, 5, 5, 5, 5, 5] 97 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 356 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758216 none CC(CN(C)C(=O)CC1(N2C=NN=N2)CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 21, 30, 30, 36, 36, 53, 77, 90, 90, 90, 90, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 30, 30, 30, 53, 53, 90, 77, 77, 77, 77, 77, 77, 77, 77] 90 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 330 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758216 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758216 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758216/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758216/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758216 Building REAL300019758217 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758217' /scratch/stefan/7898178/working/building/REAL300019758217 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758217 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758217/0 /scratch/stefan/7898178/working/building/REAL300019758217 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/31 `/scratch/stefan/7898178/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=N1) `REAL300019758217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 37, 37, 57, 57, 114, 161, 161, 200, 200, 200, 200, 10, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 57, 57, 57, 114, 114, 161, 161, 161, 161] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 10, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 37, 62, 62, 131, 131, 131, 131, 1, 21, 21, 21, 21, 21, 10, 2, 10, 10, 1, 15, 15, 15, 37, 37, 62, 62, 62, 62] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 142, 142, 142, 117, 142, 142, 96, 96, 96, 96, 96, 70, 50, 70, 29, 50, 13, 1, 13, 1, 1, 1, 1, 1, 96, 144, 144, 144, 144, 144, 142, 128, 142, 142, 96, 50, 50, 50, 29, 29, 13, 13, 13, 13] 144 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758217 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758217/1 /scratch/stefan/7898178/working/building/REAL300019758217 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/32 `/scratch/stefan/7898178/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=N1) `REAL300019758217.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 56, 56, 113, 159, 159, 200, 200, 200, 200, 10, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 56, 56, 56, 113, 113, 159, 159, 159, 159] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 10, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 37, 62, 62, 130, 130, 130, 130, 1, 21, 21, 21, 21, 21, 10, 2, 10, 10, 1, 15, 15, 15, 37, 37, 62, 62, 62, 62] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758217 none CCC1=CC=CC=C1N1C=C([O-])C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 141, 141, 141, 117, 141, 141, 96, 96, 96, 96, 96, 70, 50, 70, 29, 50, 13, 1, 13, 1, 1, 1, 1, 1, 96, 144, 144, 144, 144, 144, 141, 123, 141, 141, 96, 50, 50, 50, 29, 29, 13, 13, 13, 13] 144 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 478 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758217 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758217 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758217/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758217/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758217 Building REAL300019758218 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758218' /scratch/stefan/7898178/working/building/REAL300019758218 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758218 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758218/0 /scratch/stefan/7898178/working/building/REAL300019758218 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/33 `/scratch/stefan/7898178/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1) `REAL300019758218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758218 none CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 12, 15, 15, 20, 20, 20, 20, 1, 4, 4, 4, 4, 1, 1, 6, 6, 6, 12, 12, 15, 15, 15, 15, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 38, 22, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758218 none CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 20, 20, 20, 20, 20, 20, 16, 12, 16, 9, 12, 5, 1, 5, 1, 1, 1, 1, 1, 20, 21, 21, 21, 21, 20, 20, 12, 12, 12, 9, 9, 5, 5, 5, 5, 20] 21 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758218 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758218/1 /scratch/stefan/7898178/working/building/REAL300019758218 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/34 `/scratch/stefan/7898178/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1) `REAL300019758218.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758218 none CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 12, 15, 15, 20, 20, 20, 20, 1, 4, 4, 4, 4, 1, 1, 6, 6, 6, 12, 12, 15, 15, 15, 15, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 38, 22, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758218 none CC(=O)NC1=CNC(=O)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 20, 20, 20, 20, 20, 20, 16, 12, 16, 9, 12, 5, 1, 5, 1, 1, 1, 1, 1, 20, 21, 21, 21, 21, 20, 20, 12, 12, 12, 9, 9, 5, 5, 5, 5, 20] 21 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758218 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758218 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758218/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758218/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758218 Building REAL300019758219 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758219' /scratch/stefan/7898178/working/building/REAL300019758219 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758219 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758219/0 /scratch/stefan/7898178/working/building/REAL300019758219 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/35 `/scratch/stefan/7898178/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C(N2C=CC=C2)S1) `REAL300019758219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 24, 24, 38, 46, 46, 67, 67, 67, 67, 1, 1, 3, 3, 3, 3, 1, 2, 2, 2, 1, 24, 24, 24, 38, 38, 46, 46, 46, 46, 3, 3, 3, 3] 67 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 45, 25, 45, 17, 25, 9, 1, 9, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 17, 17, 9, 9, 9, 9, 67, 67, 67, 67] 67 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 27, 27, 41, 46, 46, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 41, 41, 46, 46, 46, 46, 1, 1, 1, 1] 66 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758219 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758219/1 /scratch/stefan/7898178/working/building/REAL300019758219 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/36 `/scratch/stefan/7898178/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C(N2C=CC=C2)S1) `REAL300019758219.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 24, 24, 38, 46, 46, 67, 67, 67, 67, 1, 1, 3, 3, 3, 3, 1, 2, 2, 2, 1, 24, 24, 24, 38, 38, 46, 46, 46, 46, 3, 3, 3, 3] 67 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 46, 25, 46, 16, 25, 8, 1, 8, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 16, 16, 8, 8, 8, 8, 67, 67, 67, 67] 67 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758219 none CC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C(N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 27, 27, 41, 46, 46, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 41, 41, 46, 46, 46, 46, 1, 1, 1, 1] 66 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758219 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758219 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758219/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758219/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758219 Building REAL300019758220 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758220' /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300019758220 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758220/0 /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/37 `/scratch/stefan/7898178/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=NN=N[N-]1) `REAL300019758220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 14, 1, 71, 117, 117, 117, 117, 71, 71, 71, 71, 51, 51, 26, 26, 26, 1, 1, 1, 11, 1] 182 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 18, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 409 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [158, 145, 114, 83, 114, 18, 83, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 18, 158, 166, 166, 166, 166, 158, 158, 158, 158, 145, 145, 114, 114, 114, 18, 18, 18, 5, 18] 166 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 552 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 22, 37, 37, 80, 80, 109, 109, 109, 109, 109, 166, 166, 166, 166, 166, 109, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 37, 37, 37, 109, 109, 109, 166, 109] 166 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 496 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758220/1 /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/38 `/scratch/stefan/7898178/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=N[N-]N=N1) `REAL300019758220.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 13, 1, 71, 124, 124, 124, 124, 71, 71, 71, 71, 51, 51, 26, 26, 26, 1, 1, 1, 11, 1] 182 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 18, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 417 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [160, 145, 113, 79, 113, 15, 79, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 15, 160, 167, 167, 167, 167, 160, 160, 160, 160, 145, 145, 113, 113, 113, 15, 15, 15, 5, 15] 167 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=NN=N[N-]2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 41, 41, 83, 83, 117, 117, 117, 117, 117, 167, 167, 167, 167, 167, 117, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 41, 41, 41, 117, 117, 117, 167, 117] 167 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `2' /scratch/stefan/7898178/working/building/REAL300019758220/2 /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 2 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/39 `/scratch/stefan/7898178/working/3D/39' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=NN=N[N-]1) `REAL300019758220.mol2' -> `2.mol2' `temp.mol2' -> `REAL300019758220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758220/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [70, 51, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 13, 1, 70, 113, 113, 113, 113, 70, 70, 70, 70, 51, 51, 26, 26, 26, 1, 1, 1, 11, 1] 179 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 18, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 396 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [155, 140, 108, 78, 108, 15, 78, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 15, 155, 163, 163, 163, 163, 155, 155, 155, 155, 140, 140, 108, 108, 108, 15, 15, 15, 5, 15] 163 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 556 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 22, 37, 37, 76, 76, 103, 103, 103, 103, 103, 162, 162, 162, 162, 162, 103, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 37, 37, 37, 103, 103, 103, 162, 103] 162 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 490 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `3' /scratch/stefan/7898178/working/building/REAL300019758220/3 /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 3 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/40 `/scratch/stefan/7898178/working/3D/40' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=N[N-]N=N1) `REAL300019758220.mol2' -> `3.mol2' `temp.mol2' -> `REAL300019758220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758220/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [69, 51, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 12, 1, 69, 117, 117, 117, 117, 69, 69, 69, 69, 51, 51, 26, 26, 26, 1, 1, 1, 11, 1] 175 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 18, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 394 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [155, 139, 106, 76, 106, 15, 76, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 15, 155, 162, 162, 162, 162, 155, 155, 155, 155, 139, 139, 106, 106, 106, 15, 15, 15, 6, 15] 162 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758220 none CC(CN(C)C(=O)C1=CC=CC(NC2=N[N-]N=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 23, 40, 40, 77, 77, 110, 110, 110, 110, 110, 162, 162, 162, 162, 162, 110, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 40, 40, 40, 110, 110, 110, 162, 110] 162 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758220 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758220 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 2: /scratch/stefan/7898178/working/building/REAL300019758220/2.* 3: /scratch/stefan/7898178/working/building/REAL300019758220/3.* 1: /scratch/stefan/7898178/working/building/REAL300019758220/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758220/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758220 Building REAL300019758221 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758221' /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300019758221 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758221/0 /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/41 `/scratch/stefan/7898178/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=NN=N[N-]1) `REAL300019758221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 13, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 16, 17, 17, 17, 17, 16, 16, 16, 16, 13, 13, 8, 8, 8, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 16, 17] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 16, 13, 10, 13, 4, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 16, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 13, 13, 13, 4, 5, 5] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 54 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [8, 1, 8, 11, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 13, 13, 13, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 60 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758221/1 /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/42 `/scratch/stefan/7898178/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=N[N-]N=N1) `REAL300019758221.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 13, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 16, 17, 17, 17, 17, 16, 16, 16, 16, 13, 13, 8, 8, 8, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 16, 17] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 16, 13, 10, 13, 4, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 16, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 13, 13, 13, 4, 5, 5] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 54 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=N[N-]N=N2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [8, 1, 8, 11, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 13, 13, 13, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 60 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `2' /scratch/stefan/7898178/working/building/REAL300019758221/2 /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 2 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/43 `/scratch/stefan/7898178/working/3D/43' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=NN=N[N-]1) `REAL300019758221.mol2' -> `2.mol2' `temp.mol2' -> `REAL300019758221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758221/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 13, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 16, 17, 17, 17, 17, 16, 16, 16, 16, 13, 13, 8, 8, 8, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 16, 17] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 15, 12, 10, 12, 4, 10, 4, 4, 5, 1, 1, 1, 1, 1, 1, 5, 5, 16, 17, 17, 17, 17, 16, 16, 16, 16, 15, 15, 12, 12, 12, 5, 5, 5] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [8, 1, 8, 11, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 13, 13, 13, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 60 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `3' /scratch/stefan/7898178/working/building/REAL300019758221/3 /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 3 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/44 `/scratch/stefan/7898178/working/3D/44' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=N[N-]N=N1) `REAL300019758221.mol2' -> `3.mol2' `temp.mol2' -> `REAL300019758221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758221/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 13, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 16, 17, 17, 17, 17, 16, 16, 16, 16, 13, 13, 8, 8, 8, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 16, 17] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [16, 15, 12, 10, 12, 4, 10, 4, 4, 5, 1, 1, 1, 1, 1, 1, 5, 5, 16, 17, 17, 17, 17, 16, 16, 16, 16, 15, 15, 12, 12, 12, 5, 5, 5] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758221 none CC(CN(C)C(=O)C1=CC=C(C2=NN=N[N-]2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 3, 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: [8, 1, 8, 11, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 13, 13, 13, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 60 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758221 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758221 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 2: /scratch/stefan/7898178/working/building/REAL300019758221/2.* 3: /scratch/stefan/7898178/working/building/REAL300019758221/3.* 1: /scratch/stefan/7898178/working/building/REAL300019758221/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758221/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758221 Building REAL300019758222 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758222' /scratch/stefan/7898178/working/building/REAL300019758222 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758222 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758222/0 /scratch/stefan/7898178/working/building/REAL300019758222 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/45 `/scratch/stefan/7898178/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=NN=N[N-]1) `REAL300019758222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=NN=N[N-]1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 196, 151, 65, 151, 29, 65, 21, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 197, 201, 201, 201, 201, 197, 197, 197, 197, 196, 196, 151, 151, 151, 29, 29, 7, 7, 4, 4, 3, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 742 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=NN=N[N-]1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 155, 70, 155, 35, 70, 28, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 155, 155, 155, 35, 35, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=NN=N[N-]1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 22, 27, 27, 28, 28, 60, 81, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 27, 27, 27, 60, 60, 95, 95, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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: 541 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758222 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758222/1 /scratch/stefan/7898178/working/building/REAL300019758222 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/46 `/scratch/stefan/7898178/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=N[N-]N=N1) `REAL300019758222.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=N[N-]N=N1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 196, 151, 65, 151, 29, 65, 21, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 197, 201, 201, 201, 201, 197, 197, 197, 197, 196, 196, 151, 151, 151, 29, 29, 7, 7, 4, 4, 3, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 742 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=N[N-]N=N1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 155, 70, 155, 35, 70, 28, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 155, 155, 155, 35, 35, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758222 none CC(CN(C)C(=O)COCC1=NC(C2=CC=CC=C2)=NO1)C1=N[N-]N=N1 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.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 22, 27, 27, 28, 28, 60, 81, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 27, 27, 27, 60, 60, 95, 95, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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: 541 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758222 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758222 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758222/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758222/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758222 Building REAL300019758223 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758223' /scratch/stefan/7898178/working/building/REAL300019758223 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758223 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758223/0 /scratch/stefan/7898178/working/building/REAL300019758223 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/47 `/scratch/stefan/7898178/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=NN=N[N-]1) `REAL300019758223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758223 none CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 16, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 158, 112, 58, 112, 29, 58, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 172, 172, 172, 172, 158, 158, 112, 112, 112, 29, 29, 5, 1, 1] 201 rigid atoms, others: [36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 783 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758223 none CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 16, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 49, 49, 81, 81, 90, 113, 113, 113, 183, 183, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 49, 49, 49, 90, 90, 113, 183, 183] 183 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 513 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758223 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758223/1 /scratch/stefan/7898178/working/building/REAL300019758223 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/48 `/scratch/stefan/7898178/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=N[N-]N=N1) `REAL300019758223.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758223 none CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 16, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 158, 112, 58, 112, 29, 58, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 172, 172, 172, 172, 158, 158, 112, 112, 112, 29, 29, 5, 1, 1] 201 rigid atoms, others: [36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 783 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758223 none CC(CN(C)C(=O)CNC(=O)C1=CN=C(Cl)C(Cl)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 8, 1, 11, 1, 1, 8, 1, 16, 1, 16, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 48, 48, 81, 81, 90, 112, 112, 112, 183, 183, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 48, 48, 48, 90, 90, 112, 183, 183] 183 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 508 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758223 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758223 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758223/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758223/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758223 Building REAL300019758224 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758224' /scratch/stefan/7898178/working/building/REAL300019758224 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758224 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758224/0 /scratch/stefan/7898178/working/building/REAL300019758224 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/49 `/scratch/stefan/7898178/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=N[N-]N=N1) `REAL300019758224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758224 none CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 21, 15, 8, 15, 1, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 25, 28, 28, 28, 28, 25, 25, 25, 25, 21, 21, 15, 15, 15, 1, 1] 28 rigid atoms, others: [5, 7, 8, 9, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758224 none CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 18, 19, 19, 25, 25, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 19, 19, 19, 28, 28] 28 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758224 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758224/1 /scratch/stefan/7898178/working/building/REAL300019758224 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/50 `/scratch/stefan/7898178/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=NN=N[N-]1) `REAL300019758224.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758224 none CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 21, 15, 8, 15, 1, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 25, 28, 28, 28, 28, 25, 25, 25, 25, 21, 21, 15, 15, 15, 1, 1] 28 rigid atoms, others: [5, 7, 8, 9, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758224 none CC(CN(C)C(=O)C1=C(C(F)(F)F)C=NN1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 18, 19, 19, 25, 25, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 19, 19, 19, 28, 28] 28 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758224 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758224 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758224/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758224/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758224 Building REAL300019758225 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758225' /scratch/stefan/7898178/working/building/REAL300019758225 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758225 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758225/0 /scratch/stefan/7898178/working/building/REAL300019758225 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/51 `/scratch/stefan/7898178/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=N[N-]N=N1) `REAL300019758225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758225 none CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 8, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [120, 111, 63, 48, 63, 13, 48, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 120, 140, 140, 140, 140, 120, 120, 120, 120, 111, 111, 64, 64, 64, 13, 13, 10, 10, 6, 6, 1] 140 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 543 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758225 none CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 8, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 22, 32, 32, 57, 57, 84, 87, 98, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 32, 32, 32, 84, 84, 87, 87, 98, 98, 110] 110 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 462 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758225 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758225/1 /scratch/stefan/7898178/working/building/REAL300019758225 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/52 `/scratch/stefan/7898178/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=NN=N[N-]1) `REAL300019758225.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758225 none CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 8, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [120, 111, 63, 48, 63, 13, 48, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 120, 140, 140, 140, 140, 120, 120, 120, 120, 111, 111, 64, 64, 64, 13, 13, 10, 10, 6, 6, 1] 140 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 543 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758225 none CC(CN(C)C(=O)CCCN1C(=O)[N-]NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 8, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 22, 32, 32, 57, 57, 84, 87, 98, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 32, 32, 32, 84, 84, 87, 87, 98, 98, 110] 110 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 462 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758225 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758225 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758225/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758225/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758225 Building REAL300019758226 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758226' /scratch/stefan/7898178/working/building/REAL300019758226 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758226 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758226/0 /scratch/stefan/7898178/working/building/REAL300019758226 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/53 `/scratch/stefan/7898178/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=NN=N[N-]1) `REAL300019758226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 1, 1, 35, 69, 69, 69, 69, 35, 35, 35, 35, 21, 21, 12, 12, 12, 1, 1, 11, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 43, 18, 19, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 258 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 178, 135, 71, 134, 17, 68, 17, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30, 200, 201, 201, 201, 201, 200, 200, 201, 201, 178, 178, 134, 134, 134, 30, 30, 9, 2, 2, 2, 1, 1, 30, 30] 201 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 816 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 27, 27, 54, 54, 62, 62, 54, 54, 172, 201, 201, 201, 201, 201, 62, 62, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 27, 27, 27, 62, 62, 172, 201, 201, 201, 201, 201, 62, 62] 201 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 590 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758226 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758226/1 /scratch/stefan/7898178/working/building/REAL300019758226 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/54 `/scratch/stefan/7898178/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=N[N-]N=N1) `REAL300019758226.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 29, 1, 1, 35, 70, 70, 70, 70, 35, 35, 35, 35, 21, 21, 12, 12, 12, 1, 1, 11, 29, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 43, 18, 19, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 258 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 178, 135, 70, 135, 16, 67, 16, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 200, 201, 201, 201, 201, 200, 200, 201, 201, 178, 178, 135, 135, 135, 29, 29, 9, 2, 2, 2, 1, 1, 29, 29] 201 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 819 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758226 none CC(CN(C)C(=O)C1=CC=C(NC2=NN(C)C=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 27, 27, 53, 53, 62, 62, 53, 53, 175, 201, 201, 201, 201, 201, 62, 62, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 27, 27, 27, 62, 62, 174, 201, 201, 201, 201, 201, 62, 62] 201 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758226 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758226 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758226/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758226/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758226 Building REAL300019758227 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758227' /scratch/stefan/7898178/working/building/REAL300019758227 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758227 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758227/0 /scratch/stefan/7898178/working/building/REAL300019758227 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/55 `/scratch/stefan/7898178/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=N[N-]N=N1) `REAL300019758227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758227 none CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 96, 62, 25, 62, 6, 25, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 107, 144, 144, 144, 144, 107, 107, 107, 107, 96, 96, 62, 62, 62, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 17, 18, 43, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 500 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758227 none CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 23, 48, 48, 82, 82, 116, 150, 150, 150, 150, 194, 194, 194, 194, 150, 150, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 48, 48, 48, 116, 116, 150, 150, 150, 150, 150, 194, 194, 150, 150, 150, 150] 194 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 839 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758227 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758227/1 /scratch/stefan/7898178/working/building/REAL300019758227 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/56 `/scratch/stefan/7898178/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=NN=N[N-]1) `REAL300019758227.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758227 none CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 94, 62, 25, 62, 6, 25, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 105, 144, 144, 144, 144, 105, 105, 105, 105, 94, 94, 62, 62, 62, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 17, 18, 43, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 498 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758227 none CC(CN(C)C(=O)CC1CCN(CC(F)(F)F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 22, 46, 46, 79, 79, 113, 147, 147, 147, 147, 193, 193, 193, 193, 147, 147, 1, 1, 1, 1, 1, 11, 11, 11, 11, 22, 22, 46, 46, 46, 113, 113, 147, 147, 147, 147, 147, 193, 193, 147, 147, 147, 147] 193 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 839 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758227 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758227 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758227/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758227/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758227 Building REAL300019758228 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758228' /scratch/stefan/7898178/working/building/REAL300019758228 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758228 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758228/0 /scratch/stefan/7898178/working/building/REAL300019758228 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/57 `/scratch/stefan/7898178/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=N[N-]N=N1) `REAL300019758228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758228 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 7, 5, 7, 1, 5, 1, 1, 7, 7, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 24, 33, 33, 33, 33, 24, 24, 24, 24, 15, 15, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 59 rigid atoms, others: [5, 7, 8, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 171 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758228 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 15, 18, 18, 24, 24, 33, 56, 56, 59, 59, 59, 59, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 18, 18, 18, 59, 59, 59, 59, 59, 59, 59, 59, 59, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 59 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 211 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758228 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758228/1 /scratch/stefan/7898178/working/building/REAL300019758228 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/58 `/scratch/stefan/7898178/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=NN=N[N-]1) `REAL300019758228.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758228 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 7, 5, 7, 1, 5, 1, 1, 7, 7, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 24, 33, 33, 33, 33, 24, 24, 24, 24, 15, 15, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 59 rigid atoms, others: [5, 7, 8, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 171 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758228 none CC(CN(C)C(=O)C1(C(=O)OC(C)(C)C)C(C)(C)C1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 15, 18, 18, 24, 24, 33, 56, 56, 59, 59, 59, 59, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 18, 18, 18, 59, 59, 59, 59, 59, 59, 59, 59, 59, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 59 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 211 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758228 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758228 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758228/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758228/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758228 Building REAL300019758229 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758229' /scratch/stefan/7898178/working/building/REAL300019758229 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758229 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758229/0 /scratch/stefan/7898178/working/building/REAL300019758229 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/59 `/scratch/stefan/7898178/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=N[N-]N=N1) `REAL300019758229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758229 none CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=N[N-]N=N1 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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [18, 14, 11, 6, 11, 3, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 11, 11, 11, 3, 9, 9, 1, 1, 1, 1, 1] 162 rigid atoms, others: [38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758229 none CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=N[N-]N=N1 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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 9, 12, 12, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 12, 12, 12, 18, 54, 54, 18, 18, 18, 18, 18] 162 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 180 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758229 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758229/1 /scratch/stefan/7898178/working/building/REAL300019758229 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/60 `/scratch/stefan/7898178/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=NN=N[N-]1) `REAL300019758229.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758229 none CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=NN=N[N-]1 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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [18, 14, 11, 6, 11, 3, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 11, 11, 11, 3, 9, 9, 1, 1, 1, 1, 1] 162 rigid atoms, others: [38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758229 none CC(CN(C)C(=O)C(O)C(O)(C1=CC=CC=C1)C(F)(F)F)C1=NN=N[N-]1 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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 9, 12, 12, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 12, 12, 12, 18, 54, 54, 18, 18, 18, 18, 18] 162 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 180 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758229 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758229 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758229/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758229/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758229 Building REAL300019758230 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758230' /scratch/stefan/7898178/working/building/REAL300019758230 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758230 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758230/0 /scratch/stefan/7898178/working/building/REAL300019758230 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/61 `/scratch/stefan/7898178/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=N[N-]N=N1) `REAL300019758230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758230 none CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 27, 27, 25, 25, 25, 25, 20, 20, 8, 8, 8, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758230 none CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 18, 18, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 18, 18, 18, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758230 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758230/1 /scratch/stefan/7898178/working/building/REAL300019758230 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/62 `/scratch/stefan/7898178/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=NN=N[N-]1) `REAL300019758230.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758230 none CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 27, 27, 25, 25, 25, 25, 20, 20, 8, 8, 8, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758230 none CC(CN(C)C(=O)C1=C2C(=CN=C1)N=CN2C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 8, 1, 8, 5, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 18, 18, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 18, 18, 18, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758230 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758230 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758230/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758230/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758230 Building REAL300019758231 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758231' /scratch/stefan/7898178/working/building/REAL300019758231 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758231 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758231/0 /scratch/stefan/7898178/working/building/REAL300019758231 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/63 `/scratch/stefan/7898178/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=NN=N[N-]1) `REAL300019758231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 12, 9, 3, 9, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 19, 23, 23, 23, 23, 19, 19, 19, 19, 12, 12, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 1, 3] 23 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 12, 9, 3, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 23, 23, 23, 23, 19, 19, 19, 19, 12, 12, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1] 23 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 13, 17, 17, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758231 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758231/1 /scratch/stefan/7898178/working/building/REAL300019758231 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/64 `/scratch/stefan/7898178/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=N[N-]N=N1) `REAL300019758231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 12, 9, 3, 9, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 19, 23, 23, 23, 23, 19, 19, 19, 19, 12, 12, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 1, 3] 23 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 12, 9, 3, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 23, 23, 23, 23, 19, 19, 19, 19, 12, 12, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1] 23 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758231 none CC(CN(C)C(=O)C1CCCN1C1=NC=CC=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 13, 17, 17, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758231 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758231 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758231/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758231/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758231 Building REAL300019758232 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758232' /scratch/stefan/7898178/working/building/REAL300019758232 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758232 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758232/0 /scratch/stefan/7898178/working/building/REAL300019758232 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/65 `/scratch/stefan/7898178/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(I)=NN1) `REAL300019758232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758232 none CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 18, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 19, 19, 36, 42, 42, 52, 52, 52, 52, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 36, 36, 42, 42, 42, 42, 1] 52 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758232 none CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 18, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 15, 14, 15, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14, 8, 8, 8, 8, 19] 19 rigid atoms, others: [8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758232 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758232/1 /scratch/stefan/7898178/working/building/REAL300019758232 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/66 `/scratch/stefan/7898178/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(I)=NN1) `REAL300019758232.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758232 none CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 18, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 19, 19, 36, 42, 42, 52, 52, 52, 52, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 36, 36, 42, 42, 42, 42, 1] 52 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758232 none CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(I)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'I', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 18, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 15, 14, 15, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14, 8, 8, 8, 8, 19] 19 rigid atoms, others: [8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758232 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758232 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758232/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758232/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758232 Building REAL300019758233 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758233' /scratch/stefan/7898178/working/building/REAL300019758233 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758233 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758233/0 /scratch/stefan/7898178/working/building/REAL300019758233 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/67 `/scratch/stefan/7898178/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=N[N-]N=N1) `REAL300019758233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 1, 1, 40, 63, 63, 63, 63, 40, 40, 40, 40, 24, 24, 16, 16, 16, 1, 1, 12, 36, 36, 36, 1, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 17, 18, 40, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 167, 129, 53, 129, 7, 53, 7, 36, 36, 7, 1, 1, 1, 1, 1, 1, 36, 36, 191, 201, 201, 201, 201, 191, 191, 191, 191, 167, 167, 125, 129, 129, 36, 36, 7, 1, 1, 1, 36, 36] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 785 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 25, 25, 50, 50, 56, 56, 51, 51, 117, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 25, 25, 25, 56, 56, 117, 201, 201, 201, 56, 56] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 569 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758233 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758233/1 /scratch/stefan/7898178/working/building/REAL300019758233 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/68 `/scratch/stefan/7898178/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=NN=N[N-]1) `REAL300019758233.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 1, 1, 40, 63, 63, 63, 63, 40, 40, 40, 40, 24, 24, 16, 16, 16, 1, 1, 12, 36, 36, 36, 1, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 17, 18, 40, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 167, 129, 53, 129, 7, 53, 7, 36, 36, 7, 1, 1, 1, 1, 1, 1, 36, 36, 191, 201, 201, 201, 201, 191, 191, 191, 191, 167, 167, 125, 129, 129, 36, 36, 7, 1, 1, 1, 36, 36] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 785 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758233 none CC(CN(C)C(=O)C1=CC=C(NN2C=CN=C2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 18, 26, 26, 50, 50, 56, 56, 51, 51, 117, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 26, 26, 26, 56, 56, 117, 201, 201, 201, 56, 56] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 568 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758233 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758233 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758233/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758233/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758233 Building REAL300019758234 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758234' /scratch/stefan/7898178/working/building/REAL300019758234 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758234 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758234/0 /scratch/stefan/7898178/working/building/REAL300019758234 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/69 `/scratch/stefan/7898178/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=N[N-]N=N1) `REAL300019758234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 43, 21, 13, 21, 11, 13, 8, 1, 1, 1, 1, 1, 1, 13, 13, 1, 69, 137, 137, 137, 137, 69, 69, 69, 69, 43, 43, 22, 22, 22, 11, 11, 8, 8, 13, 13, 13, 13, 13] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 472 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 169, 128, 95, 128, 90, 95, 78, 13, 13, 13, 13, 1, 1, 1, 1, 13, 185, 201, 201, 201, 201, 185, 185, 185, 185, 169, 169, 128, 128, 128, 90, 90, 78, 78, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 816 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 47, 47, 53, 53, 56, 58, 131, 131, 131, 131, 185, 185, 131, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 47, 47, 47, 56, 56, 58, 58, 185, 185, 185, 185, 185] 185 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 535 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758234 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758234/1 /scratch/stefan/7898178/working/building/REAL300019758234 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/70 `/scratch/stefan/7898178/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=NN=N[N-]1) `REAL300019758234.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 44, 22, 14, 22, 11, 14, 8, 1, 1, 1, 1, 1, 1, 13, 13, 1, 70, 138, 138, 138, 138, 70, 70, 70, 70, 44, 44, 23, 23, 23, 11, 11, 8, 8, 13, 13, 13, 13, 13] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 476 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 169, 128, 96, 128, 90, 96, 78, 13, 13, 13, 13, 1, 1, 1, 1, 13, 185, 201, 201, 201, 201, 185, 185, 185, 185, 169, 169, 128, 128, 128, 90, 90, 78, 78, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 819 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758234 none CC(CN(C)C(=O)CCC1=NN=C(C2CC2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 8, 8, 1, 5, 5, 5, 12, 1, 8, 8, 8, 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, 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] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 26, 48, 48, 54, 54, 57, 59, 131, 131, 131, 131, 185, 185, 131, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 48, 48, 48, 57, 57, 59, 59, 185, 185, 185, 185, 185] 185 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 538 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758234 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758234 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758234/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758234/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758234 Building REAL300019758235 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758235' /scratch/stefan/7898178/working/building/REAL300019758235 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758235 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758235/0 /scratch/stefan/7898178/working/building/REAL300019758235 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/71 `/scratch/stefan/7898178/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(C2CCOCC2)=N1) `REAL300019758235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 8, 8, 18, 18, 33, 64, 64, 124, 124, 124, 124, 1, 1, 6, 6, 6, 6, 6, 1, 11, 11, 11, 11, 11, 11, 11, 1, 18, 18, 18, 33, 33, 64, 64, 64, 64, 6, 6, 6, 6, 6, 6, 6, 6, 6] 156 rigid atoms, others: [1, 3, 4, 5, 6, 33, 18, 19, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 420 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [97, 89, 97, 89, 89, 53, 38, 53, 25, 38, 11, 1, 11, 1, 1, 1, 1, 1, 89, 89, 103, 103, 103, 103, 103, 89, 97, 97, 97, 97, 97, 97, 97, 89, 38, 38, 38, 25, 25, 11, 11, 11, 11, 103, 103, 103, 103, 103, 103, 103, 103, 103] 103 rigid atoms, others: [11, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 353 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 32, 6, 6, 6, 6, 22, 22, 48, 48, 86, 122, 122, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 6, 32, 32, 32, 32, 32, 32, 32, 6, 48, 48, 48, 86, 86, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 1, 1, 1] 156 rigid atoms, others: [51, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 669 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758235 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758235/1 /scratch/stefan/7898178/working/building/REAL300019758235 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/72 `/scratch/stefan/7898178/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(C2CCOCC2)=N1) `REAL300019758235.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 8, 8, 18, 18, 33, 64, 64, 123, 123, 123, 123, 1, 1, 6, 6, 6, 6, 6, 1, 11, 11, 11, 11, 11, 11, 11, 1, 18, 18, 18, 33, 33, 64, 64, 64, 64, 6, 6, 6, 6, 6, 6, 6, 6, 6] 159 rigid atoms, others: [1, 3, 4, 5, 6, 33, 18, 19, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 420 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [99, 90, 99, 90, 90, 53, 38, 53, 24, 38, 11, 1, 11, 1, 1, 1, 1, 1, 90, 90, 104, 104, 104, 104, 104, 90, 99, 99, 99, 99, 99, 99, 99, 90, 38, 38, 38, 24, 24, 11, 11, 11, 11, 104, 104, 104, 104, 104, 104, 104, 104, 104] 104 rigid atoms, others: [11, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 364 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758235 none CC(C)N1C=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C(C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [31, 6, 31, 6, 6, 6, 6, 22, 22, 49, 49, 87, 124, 124, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 31, 6, 49, 49, 49, 87, 87, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [51, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 670 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758235 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758235 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758235/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758235/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758235 Building REAL300019758236 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758236' /scratch/stefan/7898178/working/building/REAL300019758236 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758236 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758236/0 /scratch/stefan/7898178/working/building/REAL300019758236 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/73 `/scratch/stefan/7898178/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=N[N-]N=N1) `REAL300019758236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [55, 33, 17, 8, 17, 1, 8, 1, 1, 1, 1, 6, 9, 1, 1, 1, 5, 5, 5, 5, 5, 55, 120, 120, 120, 120, 55, 55, 55, 55, 33, 33, 17, 17, 17, 1, 6, 6, 9, 9, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 603 rigid atoms, others: [35, 5, 7, 8, 9, 10, 13, 14, 15] set([0, 1, 2, 3, 4, 6, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 409 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [104, 75, 44, 22, 44, 5, 22, 5, 5, 5, 5, 17, 24, 5, 1, 1, 1, 1, 1, 1, 1, 104, 159, 159, 159, 159, 104, 104, 104, 104, 75, 75, 44, 44, 44, 5, 17, 17, 24, 24, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 690 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 429 conformations in input total number of sets (complete confs): 429 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 41, 41, 64, 64, 95, 95, 95, 137, 138, 95, 95, 95, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 41, 41, 41, 95, 137, 137, 138, 138, 414, 110, 110, 110, 110, 110, 110, 110, 110, 110] 429 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49]) total number of confs: 996 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758236 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758236/1 /scratch/stefan/7898178/working/building/REAL300019758236 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/74 `/scratch/stefan/7898178/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=NN=N[N-]1) `REAL300019758236.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [55, 33, 17, 8, 17, 1, 8, 1, 1, 1, 1, 6, 9, 1, 1, 1, 5, 5, 5, 5, 5, 55, 120, 120, 120, 120, 55, 55, 55, 55, 33, 33, 17, 17, 17, 1, 6, 6, 9, 9, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 603 rigid atoms, others: [35, 5, 7, 8, 9, 10, 13, 14, 15] set([0, 1, 2, 3, 4, 6, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 409 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [104, 75, 44, 22, 44, 5, 22, 5, 5, 5, 5, 17, 24, 5, 1, 1, 1, 1, 1, 1, 1, 104, 159, 159, 159, 159, 104, 104, 104, 104, 75, 75, 44, 44, 44, 5, 17, 17, 24, 24, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 690 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758236 none CC(CN(C)C(=O)C1=CN(CCO)N=C1C1CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 12, 8, 1, 5, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 429 conformations in input total number of sets (complete confs): 429 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 41, 41, 64, 64, 95, 95, 95, 137, 138, 95, 95, 95, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 41, 41, 41, 95, 137, 137, 138, 138, 414, 110, 110, 110, 110, 110, 110, 110, 110, 110] 429 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49]) total number of confs: 999 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758236 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758236 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758236/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758236/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758236 Building REAL300019758237 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758237' /scratch/stefan/7898178/working/building/REAL300019758237 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758237 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758237/0 /scratch/stefan/7898178/working/building/REAL300019758237 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/75 `/scratch/stefan/7898178/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=N1) `REAL300019758237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758237 none CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 11, 11, 25, 30, 30, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 2, 1, 11, 11, 11, 25, 25, 30, 30, 30, 30, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 21, 36, 26, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758237 none CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 33, 33, 27, 21, 27, 17, 21, 8, 1, 8, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 17, 17, 8, 8, 8, 8, 33, 33] 33 rigid atoms, others: [12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 116 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758237 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758237/1 /scratch/stefan/7898178/working/building/REAL300019758237 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/76 `/scratch/stefan/7898178/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=N1) `REAL300019758237.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758237 none CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 11, 11, 25, 30, 30, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 2, 1, 11, 11, 11, 25, 25, 30, 30, 30, 30, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 21, 36, 26, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758237 none CC(=O)NC1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 33, 33, 26, 21, 26, 17, 21, 8, 1, 8, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 17, 17, 8, 8, 8, 8, 33, 33] 33 rigid atoms, others: [12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758237 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758237 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758237/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758237/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758237 Building REAL300019758238 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758238' /scratch/stefan/7898178/working/building/REAL300019758238 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758238 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758238/0 /scratch/stefan/7898178/working/building/REAL300019758238 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/77 `/scratch/stefan/7898178/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758238 none CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 11, 11, 11, 11, 1, 1, 1, 1, 1, 7, 7, 20, 20, 33, 58, 58, 106, 106, 106, 106, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 20, 20, 20, 33, 33, 58, 58, 58, 58] 122 rigid atoms, others: [0, 1, 2, 3, 40, 9, 10, 11, 12, 13, 41, 42] set([4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 375 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758238 none CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [97, 97, 97, 97, 101, 108, 108, 108, 108, 97, 97, 97, 71, 39, 71, 24, 39, 11, 1, 11, 1, 1, 1, 1, 1, 97, 97, 97, 101, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 97, 97, 97, 39, 39, 39, 24, 24, 11, 11, 11, 11] 108 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 352 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758238 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758238/1 /scratch/stefan/7898178/working/building/REAL300019758238 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/78 `/scratch/stefan/7898178/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758238 none CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 11, 11, 11, 11, 1, 1, 1, 1, 1, 7, 7, 20, 20, 34, 59, 59, 108, 108, 108, 108, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 20, 20, 20, 34, 34, 59, 59, 59, 59] 124 rigid atoms, others: [0, 1, 2, 3, 40, 9, 10, 11, 12, 13, 41, 42] set([4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 376 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758238 none CC1=C(NCC(C)(C)C)C=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 103, 110, 110, 110, 110, 99, 99, 99, 72, 39, 72, 24, 39, 10, 1, 10, 1, 1, 1, 1, 1, 99, 99, 99, 103, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 99, 99, 99, 39, 39, 39, 24, 24, 10, 10, 10, 10] 110 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 361 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758238 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758238 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758238/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758238/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758238 Building REAL300019758239 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758239' /scratch/stefan/7898178/working/building/REAL300019758239 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758239 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758239/0 /scratch/stefan/7898178/working/building/REAL300019758239 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/79 `/scratch/stefan/7898178/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=NN=N[N-]1) `REAL300019758239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 37, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 1, 47, 68, 68, 68, 68, 47, 47, 47, 47, 37, 37, 25, 25, 25, 1, 1, 1, 8, 8, 32, 32, 1] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 40, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 283 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 177, 147, 100, 147, 32, 100, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 32, 183, 201, 201, 201, 201, 183, 183, 183, 183, 177, 177, 147, 147, 147, 32, 32, 32, 9, 9, 1, 1, 32] 201 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 643 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 23, 35, 35, 46, 46, 74, 74, 46, 74, 74, 147, 201, 201, 201, 201, 74, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 35, 35, 35, 74, 74, 61, 147, 147, 201, 201, 74] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 718 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758239 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758239/1 /scratch/stefan/7898178/working/building/REAL300019758239 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/80 `/scratch/stefan/7898178/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=N[N-]N=N1) `REAL300019758239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 37, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 1, 46, 66, 66, 66, 66, 46, 46, 46, 46, 37, 37, 25, 25, 25, 1, 1, 1, 8, 8, 32, 32, 1] 201 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 40, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 178, 148, 101, 148, 32, 101, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 32, 185, 201, 201, 201, 201, 185, 185, 185, 185, 178, 178, 148, 148, 148, 32, 32, 32, 9, 9, 1, 1, 32] 201 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 649 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758239 none CC(CN(C)C(=O)C1=CC=CC(CN2C=NC=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 23, 35, 35, 46, 46, 74, 74, 46, 74, 74, 147, 201, 201, 201, 201, 74, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 35, 35, 35, 74, 74, 61, 147, 147, 201, 201, 74] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 720 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758239 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758239 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758239/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758239/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758239 Building REAL300019758240 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758240' /scratch/stefan/7898178/working/building/REAL300019758240 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758240 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758240/0 /scratch/stefan/7898178/working/building/REAL300019758240 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/81 `/scratch/stefan/7898178/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=NN=N[N-]1) `REAL300019758240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758240 none CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [55, 45, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 62, 62, 62, 62, 55, 55, 55, 55, 45, 45, 18, 18, 18, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758240 none CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 26, 39, 39, 60, 60, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 39, 39, 39, 62, 62, 62, 62] 62 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 217 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758240 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758240/1 /scratch/stefan/7898178/working/building/REAL300019758240 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/82 `/scratch/stefan/7898178/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=N[N-]N=N1) `REAL300019758240.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758240 none CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [55, 45, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 62, 62, 62, 62, 55, 55, 55, 55, 45, 45, 18, 18, 18, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758240 none CC(CN(C)C(=O)C1=NC=C2C(F)=CC=CN21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 26, 39, 39, 60, 60, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 39, 39, 39, 62, 62, 62, 62] 62 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 220 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758240 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758240 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758240/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758240/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758240 Building REAL300019758241 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758241' /scratch/stefan/7898178/working/building/REAL300019758241 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758241 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758241/0 /scratch/stefan/7898178/working/building/REAL300019758241 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/83 `/scratch/stefan/7898178/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=N[N-]N=N1) `REAL300019758241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758241 none CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 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, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 152, 106, 42, 106, 8, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 169, 169, 169, 169, 152, 152, 106, 106, 106, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 733 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758241 none CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 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, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 24, 39, 39, 68, 68, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 39, 39, 39, 130, 130, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38]) total number of confs: 643 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758241 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758241/1 /scratch/stefan/7898178/working/building/REAL300019758241 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/84 `/scratch/stefan/7898178/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=NN=N[N-]1) `REAL300019758241.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758241 none CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 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, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 151, 105, 42, 105, 8, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 201, 170, 170, 170, 170, 151, 151, 105, 105, 105, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 745 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758241 none CC(CN(C)C(=O)CC1=CNC2=CC=C(Br)C=C12)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 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, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 23, 39, 39, 68, 68, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 39, 39, 39, 130, 130, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38]) total number of confs: 644 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758241 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758241 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758241/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758241/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758241 Building REAL300019758242 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758242' /scratch/stefan/7898178/working/building/REAL300019758242 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758242 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758242/0 /scratch/stefan/7898178/working/building/REAL300019758242 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/85 `/scratch/stefan/7898178/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=N[N-]N=N1) `REAL300019758242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [40, 32, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 40, 54, 54, 54, 54, 40, 40, 40, 40, 32, 32, 12, 12, 12, 1, 1, 5, 5, 1, 5, 5] 54 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [51, 46, 23, 15, 23, 5, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 51, 54, 54, 54, 54, 51, 51, 51, 51, 46, 46, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1] 54 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [9, 1, 9, 22, 30, 30, 45, 45, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 10, 10, 10, 9, 22, 22, 30, 30, 30, 54, 54, 54, 54, 54, 54, 54] 54 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39]) total number of confs: 209 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758242 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758242/1 /scratch/stefan/7898178/working/building/REAL300019758242 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/86 `/scratch/stefan/7898178/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=NN=N[N-]1) `REAL300019758242.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [40, 32, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 40, 54, 54, 54, 54, 40, 40, 40, 40, 32, 32, 12, 12, 12, 1, 1, 5, 5, 1, 5, 5] 54 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [51, 46, 23, 15, 23, 5, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 51, 54, 54, 54, 54, 51, 51, 51, 51, 46, 46, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1] 54 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758242 none CC(CN(C)C(=O)[C@@H]1CSC(C2=CC=CC=C2)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [10, 1, 10, 22, 30, 30, 45, 45, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 10, 10, 10, 9, 22, 22, 30, 30, 30, 54, 54, 54, 54, 54, 54, 54] 54 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39]) total number of confs: 202 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758242 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758242 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758242/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758242/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758242 Building REAL300019758243 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758243' /scratch/stefan/7898178/working/building/REAL300019758243 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758243 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758243/0 /scratch/stefan/7898178/working/building/REAL300019758243 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/87 `/scratch/stefan/7898178/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=N[N-]N=N1) `REAL300019758243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758243 none CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 12, 6, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1] 39 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 33, 34, 35, 36, 37, 38, 39, 40, 42] set([0, 1, 2, 3, 4, 6, 32, 41, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758243 none CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 39, 13] 39 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758243 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758243/1 /scratch/stefan/7898178/working/building/REAL300019758243 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/88 `/scratch/stefan/7898178/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=NN=N[N-]1) `REAL300019758243.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758243 none CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 12, 6, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1] 39 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 33, 34, 35, 36, 37, 38, 39, 40, 42] set([0, 1, 2, 3, 4, 6, 32, 41, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758243 none CC(CN(C)C(=O)C1=CC2=C(CCCC2O)NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 39, 13] 39 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758243 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758243 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758243/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758243/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758243 Building REAL300019758244 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758244' /scratch/stefan/7898178/working/building/REAL300019758244 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758244 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758244/0 /scratch/stefan/7898178/working/building/REAL300019758244 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/89 `/scratch/stefan/7898178/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1) `REAL300019758244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758244 none CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 154, 103, 48, 103, 15, 48, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 164, 164, 164, 164, 154, 154, 103, 103, 103, 15, 15, 9, 9, 1, 2, 2, 1] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 736 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758244 none CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 21, 43, 43, 72, 72, 98, 107, 194, 194, 194, 194, 194, 194, 194, 194, 194, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 43, 43, 43, 98, 98, 107, 107, 194, 194, 194, 194] 194 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 561 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758244 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758244/1 /scratch/stefan/7898178/working/building/REAL300019758244 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/90 `/scratch/stefan/7898178/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1) `REAL300019758244.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758244 none CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 154, 103, 47, 103, 15, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 164, 164, 164, 164, 154, 154, 103, 103, 103, 15, 15, 9, 9, 1, 2, 2, 1] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 734 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758244 none CC(CN(C)C(=O)CCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 21, 43, 43, 73, 73, 99, 108, 195, 195, 195, 195, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 43, 43, 43, 99, 99, 108, 108, 195, 195, 195, 195] 195 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 561 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758244 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758244 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758244/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758244/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758244 Building REAL300019758245 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758245' /scratch/stefan/7898178/working/building/REAL300019758245 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758245 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758245/0 /scratch/stefan/7898178/working/building/REAL300019758245 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/91 `/scratch/stefan/7898178/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=N[N-]N=N1) `REAL300019758245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758245 none CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 208 conformations in input total number of sets (complete confs): 208 using faster count positions algorithm for large data unique positions, atoms: [46, 37, 15, 10, 15, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 52, 52, 52, 52, 46, 46, 46, 46, 37, 37, 15, 15, 15, 1, 1, 2, 2, 1] 208 rigid atoms, others: [32, 33, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 210 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758245 none CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 208 conformations in input total number of sets (complete confs): 208 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 17, 26, 26, 38, 38, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 26, 26, 26, 52, 52, 104, 104, 52] 208 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36]) total number of confs: 375 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758245 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758245/1 /scratch/stefan/7898178/working/building/REAL300019758245 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/92 `/scratch/stefan/7898178/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=NN=N[N-]1) `REAL300019758245.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758245 none CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 212 conformations in input total number of sets (complete confs): 212 using faster count positions algorithm for large data unique positions, atoms: [47, 37, 15, 10, 15, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 53, 53, 53, 53, 47, 47, 47, 47, 37, 37, 15, 15, 15, 1, 1, 2, 2, 1] 212 rigid atoms, others: [32, 33, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 216 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758245 none CC(CN(C)C(=O)C1=CC2=CC(O)=C(O)C=C2S1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 212 conformations in input total number of sets (complete confs): 212 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 18, 27, 27, 39, 39, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 27, 27, 27, 53, 53, 106, 106, 53] 212 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36]) total number of confs: 382 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758245 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758245 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758245/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758245/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758245 Building REAL300019758246 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758246' /scratch/stefan/7898178/working/building/REAL300019758246 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758246 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758246/0 /scratch/stefan/7898178/working/building/REAL300019758246 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/93 `/scratch/stefan/7898178/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CNN=C1I)C1=N[N-]N=N1) `REAL300019758246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758246 none CC(CN(C)C(=O)C1=CNN=C1I)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 8, 1, 18, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [69, 54, 25, 7, 25, 1, 7, 1, 1, 1, 1, 1, 1, 69, 82, 82, 82, 82, 69, 69, 69, 69, 54, 54, 25, 25, 25, 1, 1] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 312 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758246 none CC(CN(C)C(=O)C1=CNN=C1I)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 8, 1, 18, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 41, 41, 69, 69, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 41, 41, 41, 77, 77] 77 rigid atoms, others: [1, 13, 14, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 260 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758246 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758246/1 /scratch/stefan/7898178/working/building/REAL300019758246 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/94 `/scratch/stefan/7898178/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CNN=C1I)C1=NN=N[N-]1) `REAL300019758246.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758246 none CC(CN(C)C(=O)C1=CNN=C1I)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 8, 1, 18, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [68, 53, 25, 7, 25, 1, 7, 1, 1, 1, 1, 1, 1, 68, 81, 81, 81, 81, 68, 68, 68, 68, 53, 53, 25, 25, 25, 1, 1] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 309 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758246 none CC(CN(C)C(=O)C1=CNN=C1I)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'I', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 8, 1, 18, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 41, 41, 68, 68, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 41, 41, 41, 76, 76] 76 rigid atoms, others: [1, 13, 14, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 258 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758246 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758246 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758246/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758246/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758246 Building REAL300019758247 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758247' /scratch/stefan/7898178/working/building/REAL300019758247 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758247 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758247/0 /scratch/stefan/7898178/working/building/REAL300019758247 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/95 `/scratch/stefan/7898178/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)N=CS2)C=C1) `REAL300019758247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 6, 6, 16, 16, 24, 24, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 1, 1, 2, 2, 2, 1, 1, 4, 24, 24, 24, 29, 29, 29, 29, 29, 29, 6, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 4, 1, 1, 1, 1, 7, 7, 14, 14, 20, 25, 25, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 20, 20, 25, 25, 25, 25, 1, 6, 6] 33 rigid atoms, others: [5, 6, 7, 8, 40, 20, 21, 22] set([0, 1, 2, 3, 4, 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, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 33, 33, 33, 28, 28, 16, 11, 16, 8, 11, 5, 1, 5, 1, 1, 1, 1, 1, 28, 28, 28, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 8, 8, 5, 5, 5, 5, 28, 33, 33] 33 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758247 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758247/1 /scratch/stefan/7898178/working/building/REAL300019758247 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/96 `/scratch/stefan/7898178/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)N=CS2)C=C1) `REAL300019758247.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 6, 6, 16, 16, 24, 24, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 1, 1, 2, 2, 2, 1, 1, 4, 24, 24, 24, 29, 29, 29, 29, 29, 29, 6, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 4, 1, 1, 1, 1, 7, 7, 14, 14, 20, 25, 25, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 14, 20, 20, 25, 25, 25, 25, 1, 6, 6] 33 rigid atoms, others: [5, 6, 7, 8, 40, 20, 21, 22] set([0, 1, 2, 3, 4, 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, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758247 none CC1=CC=C(NC2=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)N=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 32, 27, 27, 15, 10, 15, 7, 10, 4, 1, 4, 1, 1, 1, 1, 1, 27, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 7, 7, 4, 4, 4, 4, 27, 32, 32] 32 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758247 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758247 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758247/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758247/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758247 Building REAL300019758248 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758248' /scratch/stefan/7898178/working/building/REAL300019758248 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758248 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758248/0 /scratch/stefan/7898178/working/building/REAL300019758248 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/97 `/scratch/stefan/7898178/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=NN=N[N-]1) `REAL300019758248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [18, 16, 6, 5, 6, 1, 5, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 18, 21, 21, 21, 21, 18, 18, 18, 18, 16, 16, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [35, 36, 5, 38, 7, 8, 39, 14, 15, 16, 40, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [18, 16, 6, 5, 6, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 18, 21, 21, 21, 21, 18, 18, 18, 18, 16, 16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 21 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [7, 1, 7, 11, 15, 15, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758248 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758248/1 /scratch/stefan/7898178/working/building/REAL300019758248 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/98 `/scratch/stefan/7898178/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=N[N-]N=N1) `REAL300019758248.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [18, 16, 6, 5, 6, 1, 5, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 18, 21, 21, 21, 21, 18, 18, 18, 18, 16, 16, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [35, 36, 5, 38, 7, 8, 39, 14, 15, 16, 40, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [18, 16, 6, 5, 6, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 18, 21, 21, 21, 21, 18, 18, 18, 18, 16, 16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 21 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758248 none CC(CN(C)C(=O)C1(C2=CC=NC=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [7, 1, 7, 11, 15, 15, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758248 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758248 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758248/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758248/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758248 Building REAL300019758249 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758249' /scratch/stefan/7898178/working/building/REAL300019758249 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758249 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758249/0 /scratch/stefan/7898178/working/building/REAL300019758249 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/99 `/scratch/stefan/7898178/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=N[N-]N=N1) `REAL300019758249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [63, 51, 32, 13, 32, 1, 13, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 63, 89, 89, 89, 89, 63, 63, 63, 63, 51, 51, 32, 32, 32, 11, 11, 11] 118 rigid atoms, others: [5, 7, 8, 9, 10, 16, 17] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 313 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [110, 105, 82, 56, 82, 11, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 110, 118, 118, 118, 118, 110, 110, 110, 110, 105, 105, 82, 82, 82, 1, 1, 1] 118 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 393 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 26, 40, 40, 66, 66, 89, 89, 89, 110, 110, 110, 110, 110, 89, 89, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 40, 40, 40, 110, 110, 110] 110 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 321 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758249 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758249/1 /scratch/stefan/7898178/working/building/REAL300019758249 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/100 `/scratch/stefan/7898178/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=NN=N[N-]1) `REAL300019758249.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [62, 50, 32, 13, 32, 1, 13, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 62, 88, 88, 88, 88, 62, 62, 62, 62, 50, 50, 32, 32, 32, 11, 11, 11] 117 rigid atoms, others: [5, 7, 8, 9, 10, 16, 17] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 311 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [109, 104, 81, 55, 81, 11, 55, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 109, 117, 117, 117, 117, 109, 109, 109, 109, 104, 104, 81, 81, 81, 1, 1, 1] 117 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 391 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758249 none CC(CN(C)C(=O)C1=NC(C2=CN=CC=N2)=NO1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 8, 8, 12, 1, 8, 8, 8, 8, 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, 3, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 26, 43, 43, 71, 71, 93, 93, 93, 114, 114, 114, 114, 114, 93, 93, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 43, 43, 43, 114, 114, 114] 114 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 341 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758249 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758249 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758249/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758249/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758249 Building REAL300019758250 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758250' /scratch/stefan/7898178/working/building/REAL300019758250 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758250 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758250/0 /scratch/stefan/7898178/working/building/REAL300019758250 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/101 `/scratch/stefan/7898178/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=N[N-]N=N1) `REAL300019758250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758250 none CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 4, 5, 1, 4, 1, 1, 1, 1, 4, 4, 8, 9, 9, 9, 1, 1, 1, 1, 7, 8, 8, 8, 8, 7, 7, 7, 7, 5, 5, 5, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 50, 47, 48, 17, 18, 19, 20, 49, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758250 none CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 8, 8, 8, 8, 9, 9, 9, 14, 14, 17, 17, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758250 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758250/1 /scratch/stefan/7898178/working/building/REAL300019758250 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/102 `/scratch/stefan/7898178/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=NN=N[N-]1) `REAL300019758250.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758250 none CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 4, 5, 1, 4, 1, 1, 1, 1, 4, 4, 8, 9, 9, 9, 1, 1, 1, 1, 7, 8, 8, 8, 8, 7, 7, 7, 7, 5, 5, 5, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 50, 47, 48, 17, 18, 19, 20, 49, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758250 none CC(CN(C)C(=O)C1CN(C(=O)OC(C)(C)C)CCN1C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 8, 8, 8, 8, 9, 9, 9, 14, 14, 17, 17, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758250 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758250 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758250/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758250/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758250 Building REAL300019758251 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758251' /scratch/stefan/7898178/working/building/REAL300019758251 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758251 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758251/0 /scratch/stefan/7898178/working/building/REAL300019758251 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/103 `/scratch/stefan/7898178/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(CC(=O)N(C)CC(C)C1=N[N-]N=N1)C(=O)OC(C)(C)C) `REAL300019758251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758251 none C#CCN(CC(=O)N(C)CC(C)C1=N[N-]N=N1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 48, 39, 17, 14, 17, 11, 14, 5, 1, 5, 1, 1, 1, 1, 1, 48, 64, 64, 66, 66, 66, 66, 49, 49, 49, 39, 39, 14, 14, 14, 11, 11, 5, 6, 6, 6, 66, 66, 66, 66, 66, 66, 66, 66, 66] 67 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 272 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758251 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758251/1 /scratch/stefan/7898178/working/building/REAL300019758251 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/104 `/scratch/stefan/7898178/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(CC(=O)N(C)CC(C)C1=NN=N[N-]1)C(=O)OC(C)(C)C) `REAL300019758251.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758251 none C#CCN(CC(=O)N(C)CC(C)C1=NN=N[N-]1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 46, 36, 17, 14, 17, 11, 14, 6, 1, 6, 1, 1, 1, 1, 1, 46, 64, 64, 66, 66, 66, 66, 47, 47, 47, 36, 36, 14, 14, 14, 11, 11, 5, 6, 6, 6, 66, 66, 66, 66, 66, 66, 66, 66, 66] 67 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 260 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758251 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758251 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758251/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758251/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758251 Building REAL300019758252 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758252' /scratch/stefan/7898178/working/building/REAL300019758252 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758252 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758252/0 /scratch/stefan/7898178/working/building/REAL300019758252 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/105 `/scratch/stefan/7898178/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=NN=N[N-]1) `REAL300019758252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 36, 16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 31, 38, 38, 36, 38, 38, 57, 119, 119, 119, 119, 57, 57, 57, 57, 36, 36, 16, 16, 16, 1, 1, 31, 31, 38, 38, 38, 38, 38] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 470 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 135, 82, 139, 38, 82, 38, 38, 38, 38, 38, 14, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 144, 144, 144, 38, 38, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 781 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 23, 47, 47, 56, 56, 82, 82, 82, 82, 82, 82, 124, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 47, 47, 47, 82, 82, 141, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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: 415 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758252 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758252/1 /scratch/stefan/7898178/working/building/REAL300019758252 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/106 `/scratch/stefan/7898178/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=N[N-]N=N1) `REAL300019758252.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 36, 16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 31, 38, 38, 36, 38, 38, 57, 119, 119, 119, 119, 57, 57, 57, 57, 36, 36, 16, 16, 16, 1, 1, 31, 31, 38, 38, 38, 38, 38] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 470 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 135, 82, 139, 38, 82, 38, 38, 38, 38, 38, 14, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 144, 144, 144, 38, 38, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 781 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758252 none CC(CN(C)C(=O)C1=NC=CN=C1SCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 1, 1, 8, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 22, 46, 46, 55, 55, 81, 81, 81, 81, 81, 81, 123, 140, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 46, 46, 46, 81, 81, 140, 140, 140, 140, 140, 140, 140] 140 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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: 412 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758252 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758252 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758252/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758252/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758252 Building REAL300019758253 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758253' /scratch/stefan/7898178/working/building/REAL300019758253 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758253 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758253/0 /scratch/stefan/7898178/working/building/REAL300019758253 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/107 `/scratch/stefan/7898178/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=N[N-]N=N1) `REAL300019758253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758253 none CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 1, 8, 8, 8, 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, 6, 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] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [53, 47, 32, 15, 32, 6, 15, 1, 1, 1, 1, 1, 1, 1, 1, 53, 62, 62, 62, 62, 53, 53, 53, 53, 47, 47, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 228 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758253 none CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 1, 8, 8, 8, 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, 6, 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] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 11, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758253 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758253/1 /scratch/stefan/7898178/working/building/REAL300019758253 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/108 `/scratch/stefan/7898178/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=NN=N[N-]1) `REAL300019758253.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758253 none CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 1, 8, 8, 8, 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, 6, 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] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [53, 47, 32, 15, 32, 6, 15, 1, 1, 1, 1, 1, 1, 1, 1, 53, 62, 62, 62, 62, 53, 53, 53, 53, 47, 47, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 228 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758253 none CC(CN(C)C(=O)CC1CCCS1(=O)=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 1, 8, 8, 8, 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, 6, 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] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 11, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758253 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758253 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758253/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758253/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758253 Building REAL300019758254 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758254' /scratch/stefan/7898178/working/building/REAL300019758254 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758254 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758254/0 /scratch/stefan/7898178/working/building/REAL300019758254 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/109 `/scratch/stefan/7898178/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=N[N-]N=N1) `REAL300019758254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758254 none CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758254 none CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 20, 20, 24, 24, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 20, 20, 20, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 102 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758254 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758254/1 /scratch/stefan/7898178/working/building/REAL300019758254 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/110 `/scratch/stefan/7898178/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=NN=N[N-]1) `REAL300019758254.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758254 none CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758254 none CC(CN(C)C(=O)C1=CC2=CC=CC=C2OC1C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 20, 20, 24, 24, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 20, 20, 20, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 102 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758254 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758254 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758254/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758254/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758254 Building REAL300019758255 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758255' /scratch/stefan/7898178/working/building/REAL300019758255 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758255 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758255/0 /scratch/stefan/7898178/working/building/REAL300019758255 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/111 `/scratch/stefan/7898178/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1) `REAL300019758255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758255 none CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 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, 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, 1, 4, 4, 6, 6, 19, 19, 24, 24, 31, 33, 33, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 1, 6, 6, 24, 24, 24, 31, 31, 33, 33, 33, 33, 1, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758255 none CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 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, 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: [34, 34, 34, 34, 34, 28, 34, 28, 17, 14, 17, 9, 14, 6, 1, 6, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 28, 28, 14, 14, 14, 9, 9, 6, 6, 6, 6, 34, 34] 34 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 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: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758255 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758255/1 /scratch/stefan/7898178/working/building/REAL300019758255 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/112 `/scratch/stefan/7898178/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1) `REAL300019758255.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758255 none CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 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, 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, 1, 4, 4, 6, 6, 19, 19, 24, 24, 31, 33, 33, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 1, 6, 6, 24, 24, 24, 31, 31, 33, 33, 33, 33, 1, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758255 none CC1=CC=C(C(=O)C=CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 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, 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: [34, 34, 34, 34, 34, 28, 34, 28, 17, 14, 17, 9, 14, 6, 1, 6, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 28, 28, 14, 14, 14, 9, 9, 6, 6, 6, 6, 34, 34] 34 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 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: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758255 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758255 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758255/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758255/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758255 Building REAL300019758256 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758256' /scratch/stefan/7898178/working/building/REAL300019758256 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758256 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758256/0 /scratch/stefan/7898178/working/building/REAL300019758256 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/113 `/scratch/stefan/7898178/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=N[N-]N=N1) `REAL300019758256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758256 none CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 15, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 16, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 23, 18, 18, 18, 18, 16, 16, 7, 7, 7, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758256 none CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 15, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 12, 17, 17, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 17, 17, 17, 23, 23, 23, 23] 23 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758256 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758256/1 /scratch/stefan/7898178/working/building/REAL300019758256 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/114 `/scratch/stefan/7898178/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=NN=N[N-]1) `REAL300019758256.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758256 none CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 15, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 16, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 23, 18, 18, 18, 18, 16, 16, 7, 7, 7, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758256 none CC(CN(C)C(=O)C1=CC=C2NC=NC2=C1F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 15, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 12, 17, 17, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 17, 17, 17, 23, 23, 23, 23] 23 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758256 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758256 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758256/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758256/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758256 Building REAL300019758257 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758257' /scratch/stefan/7898178/working/building/REAL300019758257 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758257 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758257/0 /scratch/stefan/7898178/working/building/REAL300019758257 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/115 `/scratch/stefan/7898178/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=NN=N[N-]1) `REAL300019758257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 12, 9, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 9, 9, 9, 1, 1, 1, 9, 9, 1] 28 rigid atoms, others: [33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 12, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 62 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 25, 24, 25, 9, 24, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 25, 25, 25, 9, 9, 9, 1, 1, 9] 28 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 74 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 18, 29, 29, 37, 37, 52, 52, 52, 52, 52, 82, 82, 82, 82, 82, 52, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 29, 29, 29, 52, 52, 52, 82, 82, 52] 82 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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: 214 number of broken/clashed sets: 80 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758257 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758257/1 /scratch/stefan/7898178/working/building/REAL300019758257 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/116 `/scratch/stefan/7898178/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=N[N-]N=N1) `REAL300019758257.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 12, 9, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 9, 9, 9, 1, 1, 1, 9, 9, 1] 28 rigid atoms, others: [33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 12, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 68 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 25, 24, 25, 9, 24, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 25, 25, 25, 9, 9, 9, 1, 1, 9] 28 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 74 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758257 none CC(CN(C)C(=O)C1=CC=CC(N2N=NN=C2N)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 18, 29, 29, 38, 38, 52, 52, 52, 52, 52, 82, 82, 82, 82, 82, 52, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 29, 29, 29, 52, 52, 52, 82, 82, 52] 82 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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: 216 number of broken/clashed sets: 80 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758257 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758257 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758257/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758257/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758257 Building REAL300019758258 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758258' /scratch/stefan/7898178/working/building/REAL300019758258 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758258 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758258/0 /scratch/stefan/7898178/working/building/REAL300019758258 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/117 `/scratch/stefan/7898178/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)N=CS1) `REAL300019758258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 51, 51, 121, 121, 182, 201, 201, 201, 201, 201, 201, 18, 18, 18, 2, 2, 2, 1, 1, 1, 1, 7, 121, 121, 121, 182, 182, 201, 201, 201, 201, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 7, 18, 18, 7, 1, 1, 1, 1, 8, 8, 28, 28, 54, 85, 85, 148, 148, 148, 148, 1, 1, 1, 18, 18, 18, 18, 10, 18, 18, 7, 28, 28, 28, 54, 54, 85, 85, 85, 85, 1] 201 rigid atoms, others: [7, 8, 9, 10, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 174, 201, 201, 174, 154, 154, 99, 58, 99, 29, 58, 12, 1, 12, 1, 1, 1, 1, 1, 154, 154, 154, 201, 201, 201, 201, 200, 201, 201, 174, 58, 58, 58, 29, 29, 12, 12, 12, 12, 154] 201 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758258 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758258/1 /scratch/stefan/7898178/working/building/REAL300019758258 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/118 `/scratch/stefan/7898178/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)N=CS1) `REAL300019758258.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 51, 51, 121, 121, 182, 201, 201, 201, 201, 201, 201, 18, 18, 18, 2, 2, 2, 1, 1, 1, 1, 7, 121, 121, 121, 182, 182, 201, 201, 201, 201, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 7, 18, 18, 7, 1, 1, 1, 1, 8, 8, 28, 28, 54, 85, 85, 148, 148, 148, 148, 1, 1, 1, 18, 18, 18, 18, 10, 18, 18, 7, 28, 28, 28, 54, 54, 85, 85, 85, 85, 1] 201 rigid atoms, others: [7, 8, 9, 10, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758258 none CC1=CC=CC=C1NC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 175, 201, 201, 175, 155, 155, 100, 58, 100, 29, 58, 12, 1, 12, 1, 1, 1, 1, 1, 155, 155, 155, 201, 201, 201, 201, 200, 201, 201, 175, 58, 58, 58, 29, 29, 12, 12, 12, 12, 155] 201 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 692 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758258 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758258 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758258/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758258/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758258 Building REAL300019758259 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758259' /scratch/stefan/7898178/working/building/REAL300019758259 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758259 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758259/0 /scratch/stefan/7898178/working/building/REAL300019758259 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/119 `/scratch/stefan/7898178/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758259 none CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.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, 17, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 56, 70, 70, 88, 88, 88, 88, 3, 3, 3, 3, 3, 1, 25, 25, 25, 56, 56, 70, 70, 70, 70] 108 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 329 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758259 none CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.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, 17, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 47, 47, 47, 47, 47, 47, 44, 34, 44, 25, 34, 12, 1, 12, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 47, 34, 34, 34, 25, 25, 12, 12, 12, 12] 59 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 247 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758259 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758259/1 /scratch/stefan/7898178/working/building/REAL300019758259 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/120 `/scratch/stefan/7898178/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758259.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758259 none CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.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, 17, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 56, 70, 70, 88, 88, 88, 88, 3, 3, 3, 3, 3, 1, 25, 25, 25, 56, 56, 70, 70, 70, 70] 108 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 329 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758259 none CCN1C(Br)=NC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'Br', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.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, 17, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 47, 47, 47, 47, 47, 47, 44, 34, 44, 25, 34, 11, 1, 11, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 47, 34, 34, 34, 25, 25, 11, 11, 11, 11] 60 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758259 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758259 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758259/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758259/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758259 Building REAL300019758260 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758260' /scratch/stefan/7898178/working/building/REAL300019758260 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758260 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758260/0 /scratch/stefan/7898178/working/building/REAL300019758260 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/121 `/scratch/stefan/7898178/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=N[N-]N=N1) `REAL300019758260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758260 none CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 5, 7, 1, 5, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 16, 19, 19, 19, 19, 16, 16, 16, 16, 13, 13, 7, 7, 7, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758260 none CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 14, 14, 14, 19, 19, 19] 19 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758260 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758260/1 /scratch/stefan/7898178/working/building/REAL300019758260 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/122 `/scratch/stefan/7898178/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=NN=N[N-]1) `REAL300019758260.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758260 none CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 5, 7, 1, 5, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 16, 19, 19, 19, 19, 16, 16, 16, 16, 13, 13, 7, 7, 7, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758260 none CC(CN(C)C(=O)C1=CC(C(F)(F)F)=CNC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 14, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 14, 14, 14, 19, 19, 19] 19 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758260 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758260 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758260/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758260/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758260 Building REAL300019758261 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758261' /scratch/stefan/7898178/working/building/REAL300019758261 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758261 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758261/0 /scratch/stefan/7898178/working/building/REAL300019758261 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/123 `/scratch/stefan/7898178/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=N[N-]N=N1) `REAL300019758261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758261 none CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 37, 37, 37, 29, 37, 19, 29, 38, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 42, 37, 37, 37, 29, 38, 38, 114, 19, 4, 4, 1, 1, 1, 1, 1] 129 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 331 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758261 none CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 8, 9, 9, 9, 9, 13, 19, 13, 18, 20, 20, 20, 36, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 9, 9, 9, 13, 19, 19, 57, 18, 36, 36, 40, 40, 40, 40, 40] 120 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46]) total number of confs: 242 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758261 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758261/1 /scratch/stefan/7898178/working/building/REAL300019758261 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/124 `/scratch/stefan/7898178/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=NN=N[N-]1) `REAL300019758261.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758261 none CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 37, 37, 37, 29, 37, 19, 29, 38, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 42, 42, 37, 37, 37, 29, 38, 38, 114, 19, 4, 4, 1, 1, 1, 1, 1] 129 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 331 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758261 none CC(CN(C)C(=O)C(CO)NC(=O)OCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 12, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 9, 10, 10, 10, 10, 13, 19, 13, 18, 20, 20, 20, 36, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 10, 10, 10, 13, 19, 19, 57, 18, 36, 36, 40, 40, 40, 40, 40] 120 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758261 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758261 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758261/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758261/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758261 Building REAL300019758262 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758262' /scratch/stefan/7898178/working/building/REAL300019758262 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758262 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758262/0 /scratch/stefan/7898178/working/building/REAL300019758262 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/125 `/scratch/stefan/7898178/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=NN=N[N-]1) `REAL300019758262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758262 none CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [35, 27, 12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 38, 38, 38, 38, 35, 35, 35, 35, 27, 27, 12, 12, 12, 1, 1, 1, 1] 38 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758262 none CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 15, 18, 18, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 18, 18, 18, 38, 38, 38, 38] 38 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758262 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758262/1 /scratch/stefan/7898178/working/building/REAL300019758262 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/126 `/scratch/stefan/7898178/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=N[N-]N=N1) `REAL300019758262.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758262 none CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [35, 27, 12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 38, 38, 38, 38, 35, 35, 35, 35, 27, 27, 12, 12, 12, 1, 1, 1, 1] 38 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758262 none CC(CN(C)C(=O)C1=CN2C=CN=C2C(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 16, 19, 19, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 19, 19, 19, 38, 38, 38, 38] 38 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758262 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758262 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758262/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758262/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758262 Building REAL300019758263 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758263' /scratch/stefan/7898178/working/building/REAL300019758263 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758263 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758263/0 /scratch/stefan/7898178/working/building/REAL300019758263 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/127 `/scratch/stefan/7898178/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=N[N-]N=N1) `REAL300019758263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758263 none CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 19 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 47, 48, 49, 50, 20, 21, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758263 none CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 12, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 27, 27, 34, 34, 34, 34, 16, 16, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 15, 15, 15, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 16, 16, 16, 16] 34 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758263 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758263/1 /scratch/stefan/7898178/working/building/REAL300019758263 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/128 `/scratch/stefan/7898178/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=NN=N[N-]1) `REAL300019758263.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758263 none CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 19 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 13, 47, 48, 49, 50, 20, 21, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758263 none CC(CN(C)C(=O)C1=NOC2(CN(C(=O)OC(C)(C)C)C2)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 13, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 28, 28, 34, 34, 34, 34, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 16, 16, 16, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17] 34 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758263 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758263 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758263/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758263/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758263 Building REAL300019758264 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758264' /scratch/stefan/7898178/working/building/REAL300019758264 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758264 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758264/0 /scratch/stefan/7898178/working/building/REAL300019758264 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/129 `/scratch/stefan/7898178/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=NN=N[N-]1) `REAL300019758264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758264 none CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 18, 8, 8, 5, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 26, 16, 9, 16, 1, 9, 1, 1, 1, 1, 1, 1, 1, 33, 38, 38, 38, 38, 33, 33, 33, 33, 26, 26, 16, 16, 16, 1, 2, 2, 2] 38 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758264 none CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 18, 8, 8, 5, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 11, 15, 15, 30, 30, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 15, 15, 15, 38, 38, 38, 38] 38 rigid atoms, others: [1, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758264 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758264/1 /scratch/stefan/7898178/working/building/REAL300019758264 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/130 `/scratch/stefan/7898178/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=N[N-]N=N1) `REAL300019758264.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758264 none CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 18, 8, 8, 5, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 26, 16, 9, 16, 1, 9, 1, 1, 1, 1, 1, 1, 1, 33, 38, 38, 38, 38, 33, 33, 33, 33, 26, 26, 16, 16, 16, 1, 2, 2, 2] 38 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758264 none CC(CN(C)C(=O)C1=CC(I)=NN1C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 18, 8, 8, 5, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 11, 15, 15, 30, 30, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 15, 15, 15, 38, 38, 38, 38] 38 rigid atoms, others: [1, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758264 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758264 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758264/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758264/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758264 Building REAL300019758265 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758265' /scratch/stefan/7898178/working/building/REAL300019758265 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758265 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758265/0 /scratch/stefan/7898178/working/building/REAL300019758265 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/131 `/scratch/stefan/7898178/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=N[N-]N=N1) `REAL300019758265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758265 none CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 4, 3, 4, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 7, 7, 7, 7, 6, 6, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 8 rigid atoms, others: [38, 7, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 34 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758265 none CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758265 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758265/1 /scratch/stefan/7898178/working/building/REAL300019758265 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/132 `/scratch/stefan/7898178/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=NN=N[N-]1) `REAL300019758265.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758265 none CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 4, 3, 4, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 7, 7, 7, 7, 6, 6, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 8 rigid atoms, others: [38, 7, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 34 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758265 none CC(CN(C)C(=O)C(C)(C)C1=CC=C(C#N)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758265 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758265 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758265/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758265/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758265 Building REAL300019758266 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758266' /scratch/stefan/7898178/working/building/REAL300019758266 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758266 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758266/0 /scratch/stefan/7898178/working/building/REAL300019758266 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/133 `/scratch/stefan/7898178/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=N[N-]N=N1) `REAL300019758266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758266 none CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 21, 23, 23, 23, 1, 1, 36, 62, 62, 62, 62, 36, 36, 36, 36, 25, 25, 16, 16, 16, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 51, 52, 21, 22, 39, 54, 53, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 259 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758266 none CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 16, 24, 24, 41, 41, 56, 56, 56, 56, 56, 56, 113, 157, 157, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 24, 24, 24, 56, 56, 56, 56, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 56] 201 rigid atoms, others: [1, 23, 24, 25, 26, 27] set([0, 2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 650 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758266 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758266/1 /scratch/stefan/7898178/working/building/REAL300019758266 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/134 `/scratch/stefan/7898178/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=NN=N[N-]1) `REAL300019758266.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758266 none CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 21, 23, 23, 23, 1, 1, 36, 62, 62, 62, 62, 36, 36, 36, 36, 25, 25, 16, 16, 16, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 51, 52, 21, 22, 39, 54, 53, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 259 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758266 none CC(CN(C)C(=O)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 16, 24, 24, 41, 41, 56, 56, 56, 56, 56, 56, 112, 157, 157, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 24, 24, 24, 56, 56, 56, 56, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 56] 201 rigid atoms, others: [1, 23, 24, 25, 26, 27] set([0, 2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 650 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758266 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758266 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758266/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758266/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758266 Building REAL300019758267 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758267' /scratch/stefan/7898178/working/building/REAL300019758267 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758267 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758267/0 /scratch/stefan/7898178/working/building/REAL300019758267 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/135 `/scratch/stefan/7898178/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758267 none CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 96, 96, 126, 137, 137, 166, 166, 166, 166, 10, 10, 10, 10, 1, 1, 96, 96, 96, 126, 126, 137, 137, 137, 137] 166 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758267 none CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [84, 57, 84, 84, 119, 119, 119, 119, 119, 34, 57, 23, 34, 10, 1, 10, 1, 1, 1, 1, 1, 84, 84, 84, 84, 119, 119, 34, 34, 34, 23, 23, 10, 10, 10, 10] 119 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758267 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758267/1 /scratch/stefan/7898178/working/building/REAL300019758267 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/136 `/scratch/stefan/7898178/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758267.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758267 none CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 94, 94, 124, 136, 136, 163, 163, 163, 163, 10, 10, 10, 10, 1, 1, 94, 94, 94, 124, 124, 136, 136, 136, 136] 163 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758267 none CC(=CC1=CC=C(Br)O1)C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [86, 59, 86, 86, 120, 120, 120, 120, 120, 35, 59, 24, 35, 10, 1, 10, 1, 1, 1, 1, 1, 86, 86, 86, 86, 120, 120, 35, 35, 35, 24, 24, 10, 10, 10, 10] 120 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758267 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758267 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758267/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758267/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758267 Building REAL300019758268 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758268' /scratch/stefan/7898178/working/building/REAL300019758268 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758268 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758268/0 /scratch/stefan/7898178/working/building/REAL300019758268 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/137 `/scratch/stefan/7898178/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=NN=N[N-]1) `REAL300019758268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 22, 9, 22, 1, 9, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 1, 42, 67, 67, 67, 67, 42, 42, 42, 42, 29, 29, 22, 22, 22, 1, 1, 1, 28, 28, 28, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 20, 41, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 251 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 161, 104, 161, 28, 104, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 161, 161, 161, 28, 28, 28, 1, 1, 1, 28] 201 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 666 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 18, 30, 30, 41, 41, 71, 71, 71, 71, 71, 163, 201, 201, 201, 201, 201, 201, 71, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 30, 30, 30, 71, 71, 71, 201, 201, 201, 71] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 401 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758268 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758268/1 /scratch/stefan/7898178/working/building/REAL300019758268 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/138 `/scratch/stefan/7898178/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=N[N-]N=N1) `REAL300019758268.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 22, 9, 22, 1, 9, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 1, 42, 67, 67, 67, 67, 42, 42, 42, 42, 29, 29, 22, 22, 22, 1, 1, 1, 28, 28, 28, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 20, 41, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 251 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 161, 103, 161, 28, 103, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 161, 161, 161, 28, 28, 28, 1, 1, 1, 28] 201 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 668 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758268 none CC(CN(C)C(=O)C1=CC=CC(OC2=CC=C(Cl)C=N2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 18, 30, 30, 41, 41, 72, 72, 72, 72, 72, 163, 201, 201, 201, 201, 201, 201, 72, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 30, 30, 30, 72, 72, 72, 201, 201, 201, 72] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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]) total number of confs: 401 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758268 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758268 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758268/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758268/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758268 Building REAL300019758269 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758269' /scratch/stefan/7898178/working/building/REAL300019758269 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758269 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758269/0 /scratch/stefan/7898178/working/building/REAL300019758269 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/139 `/scratch/stefan/7898178/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=N[N-]N=N1) `REAL300019758269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758269 none CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [65, 48, 30, 9, 30, 1, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 65, 81, 81, 81, 81, 65, 65, 65, 65, 48, 48, 30, 30, 30, 1, 1, 3, 1, 1, 1] 81 rigid atoms, others: [32, 33, 35, 36, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 304 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758269 none CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 24, 37, 37, 46, 46, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 37, 37, 37, 81, 81, 81, 81, 81, 81] 81 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37]) total number of confs: 228 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758269 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758269/1 /scratch/stefan/7898178/working/building/REAL300019758269 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/140 `/scratch/stefan/7898178/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=NN=N[N-]1) `REAL300019758269.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758269 none CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [65, 48, 30, 9, 30, 1, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 65, 82, 82, 82, 82, 65, 65, 65, 65, 48, 48, 30, 30, 30, 1, 1, 3, 1, 1, 1] 82 rigid atoms, others: [32, 33, 35, 36, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 306 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758269 none CC(CN(C)C(=O)C1=CC=C2C(C=O)=CNC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 11, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 24, 37, 37, 47, 47, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 37, 37, 37, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37]) total number of confs: 232 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758269 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758269 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758269/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758269/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758269 Building REAL300019758270 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758270' /scratch/stefan/7898178/working/building/REAL300019758270 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758270 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758270/0 /scratch/stefan/7898178/working/building/REAL300019758270 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/141 `/scratch/stefan/7898178/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=C1C) `REAL300019758270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 3, 13, 13, 45, 45, 78, 122, 122, 132, 132, 132, 132, 2, 2, 2, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 45, 45, 45, 78, 78, 122, 122, 122, 122, 2, 3, 3, 3, 3] 132 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 31] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 562 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 2, 4, 2, 3, 1, 1, 1, 1, 1, 7, 7, 25, 25, 43, 73, 73, 104, 104, 104, 104, 1, 1, 1, 1, 3, 3, 3, 2, 4, 3, 3, 3, 1, 25, 25, 25, 43, 43, 73, 73, 73, 73, 1, 1, 2, 2, 2] 132 rigid atoms, others: [36, 8, 9, 10, 11, 12, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 393 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 105, 105, 83, 83, 83, 56, 38, 56, 26, 38, 11, 1, 11, 1, 1, 1, 1, 1, 83, 83, 83, 83, 105, 105, 105, 105, 105, 105, 105, 105, 83, 38, 38, 38, 26, 26, 11, 11, 11, 11, 83, 83, 83, 83, 83] 105 rigid atoms, others: [17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758270 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758270/1 /scratch/stefan/7898178/working/building/REAL300019758270 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/142 `/scratch/stefan/7898178/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=C1C) `REAL300019758270.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 3, 13, 13, 45, 45, 78, 122, 122, 133, 133, 133, 133, 2, 2, 2, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 45, 45, 45, 78, 78, 122, 122, 122, 122, 2, 3, 3, 3, 3] 133 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 31] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 567 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 2, 4, 2, 3, 1, 1, 1, 1, 1, 7, 7, 25, 25, 43, 74, 74, 105, 105, 105, 105, 1, 1, 1, 1, 3, 3, 3, 2, 4, 3, 3, 3, 1, 25, 25, 25, 43, 43, 74, 74, 74, 74, 1, 1, 2, 2, 2] 133 rigid atoms, others: [36, 8, 9, 10, 11, 12, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 399 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758270 none CC1=CC(C=O)=C(C)N1C1=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 82, 82, 82, 57, 37, 57, 26, 37, 11, 1, 11, 1, 1, 1, 1, 1, 82, 82, 82, 82, 107, 107, 107, 107, 107, 107, 107, 107, 82, 37, 37, 37, 26, 26, 11, 11, 11, 11, 82, 82, 82, 82, 82] 107 rigid atoms, others: [17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 313 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758270 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758270 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758270/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758270/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758270 Building REAL300019758271 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758271' /scratch/stefan/7898178/working/building/REAL300019758271 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758271 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758271/0 /scratch/stefan/7898178/working/building/REAL300019758271 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/143 `/scratch/stefan/7898178/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1) `REAL300019758271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 63, 63, 107, 157, 157, 179, 179, 179, 179, 7, 2, 2, 2, 1, 3, 2, 2, 2, 7, 7, 7, 63, 63, 63, 107, 107, 157, 157, 157, 157, 7] 179 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 30] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 744 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 32, 51, 51, 87, 87, 87, 87, 1, 7, 7, 7, 7, 14, 7, 7, 7, 1, 1, 1, 17, 17, 17, 32, 32, 51, 51, 51, 51, 1] 179 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 317 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 113, 56, 56, 56, 56, 56, 39, 35, 39, 25, 35, 10, 1, 10, 1, 1, 1, 1, 1, 56, 113, 113, 113, 113, 113, 113, 113, 113, 56, 56, 56, 35, 35, 35, 25, 25, 10, 10, 10, 10, 56] 113 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 264 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758271 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758271/1 /scratch/stefan/7898178/working/building/REAL300019758271 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/144 `/scratch/stefan/7898178/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1) `REAL300019758271.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 64, 64, 108, 158, 158, 180, 180, 180, 180, 7, 2, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 64, 64, 64, 108, 108, 158, 158, 158, 158, 7] 180 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 30] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 747 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 32, 52, 52, 92, 92, 92, 92, 1, 7, 7, 7, 7, 13, 7, 7, 7, 1, 1, 1, 17, 17, 17, 32, 32, 52, 52, 52, 52, 1] 180 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 327 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758271 none CC1=CC(C=O)=C(C)N1C1=CC=CC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 113, 56, 56, 56, 56, 56, 39, 35, 39, 26, 35, 11, 1, 11, 1, 1, 1, 1, 1, 56, 113, 113, 113, 113, 113, 113, 113, 113, 56, 56, 56, 35, 35, 35, 26, 26, 11, 11, 11, 11, 56] 113 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758271 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758271 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758271/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758271/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758271 Building REAL300019758272 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758272' /scratch/stefan/7898178/working/building/REAL300019758272 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758272 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758272/0 /scratch/stefan/7898178/working/building/REAL300019758272 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/145 `/scratch/stefan/7898178/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 15, 15, 23, 23, 38, 53, 53, 65, 65, 65, 65, 2, 2, 2, 1, 3, 2, 2, 2, 5, 5, 4, 5, 23, 23, 23, 38, 38, 53, 53, 53, 53] 65 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 30] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 264 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 28, 39, 39, 53, 53, 53, 53, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 17, 17, 17, 28, 28, 39, 39, 39, 39] 65 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 62, 51, 51, 51, 44, 51, 51, 39, 32, 39, 24, 32, 12, 1, 12, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 51, 51, 51, 51, 32, 32, 32, 24, 24, 12, 12, 12, 12] 62 rigid atoms, others: [20, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758272 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758272/1 /scratch/stefan/7898178/working/building/REAL300019758272 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/146 `/scratch/stefan/7898178/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758272.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 15, 15, 23, 23, 38, 53, 53, 66, 66, 66, 66, 2, 2, 2, 1, 4, 2, 2, 2, 5, 5, 4, 5, 23, 23, 23, 38, 38, 53, 53, 53, 53] 66 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 30] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 28, 39, 39, 54, 54, 54, 54, 5, 5, 5, 5, 11, 5, 5, 5, 1, 1, 1, 1, 17, 17, 17, 28, 28, 39, 39, 39, 39] 66 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758272 none CC1=CC(C=O)=C(C)N1C1=CC=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [63, 63, 63, 63, 63, 63, 63, 63, 52, 52, 52, 44, 52, 52, 40, 32, 40, 24, 32, 12, 1, 12, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 52, 52, 52, 52, 32, 32, 32, 24, 24, 12, 12, 12, 12] 63 rigid atoms, others: [20, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758272 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758272 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758272/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758272/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758272 Building REAL300019758273 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758273' /scratch/stefan/7898178/working/building/REAL300019758273 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758273 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758273/0 /scratch/stefan/7898178/working/building/REAL300019758273 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/147 `/scratch/stefan/7898178/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1) `REAL300019758273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 4, 2, 3, 20, 52, 52, 56, 56, 129, 188, 188, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 3, 2, 2, 2, 4, 4, 20, 20, 56, 56, 56, 129, 129, 188, 188, 188, 188, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 31] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 4, 4, 1, 1, 1, 1, 1, 1, 8, 20, 20, 22, 22, 57, 93, 93, 119, 119, 119, 119, 1, 1, 4, 4, 4, 4, 8, 4, 4, 4, 1, 1, 8, 8, 23, 23, 23, 57, 57, 93, 93, 93, 93, 1, 1] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 49, 50, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 177, 177, 177, 177, 122, 114, 122, 122, 78, 27, 27, 27, 20, 27, 11, 1, 11, 1, 1, 1, 1, 1, 122, 122, 177, 177, 177, 177, 177, 177, 177, 177, 122, 122, 78, 78, 27, 27, 27, 20, 20, 11, 11, 11, 11, 122, 122] 177 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758273 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758273/1 /scratch/stefan/7898178/working/building/REAL300019758273 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/148 `/scratch/stefan/7898178/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1) `REAL300019758273.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 4, 4, 2, 3, 20, 52, 52, 56, 56, 129, 188, 188, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 2, 2, 2, 2, 4, 4, 20, 20, 56, 56, 56, 129, 129, 188, 188, 188, 188, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 6, 7, 8, 9, 31] set([5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 7, 4, 4, 1, 1, 1, 1, 1, 1, 8, 20, 20, 22, 22, 56, 92, 92, 118, 118, 118, 118, 1, 1, 4, 4, 4, 4, 7, 4, 4, 4, 1, 1, 8, 8, 23, 23, 23, 56, 56, 92, 92, 92, 92, 1, 1] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 49, 50, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758273 none CC1=CC(C=O)=C(C)N1C1=CC=C(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 1, 5, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 179, 179, 179, 124, 113, 124, 124, 78, 28, 28, 28, 20, 28, 11, 1, 11, 1, 1, 1, 1, 1, 124, 124, 179, 179, 179, 179, 179, 179, 179, 179, 124, 124, 78, 78, 28, 28, 28, 20, 20, 11, 11, 11, 11, 124, 124] 179 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758273 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758273 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758273/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758273/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758273 Building REAL300019758274 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758274' /scratch/stefan/7898178/working/building/REAL300019758274 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758274 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758274/0 /scratch/stefan/7898178/working/building/REAL300019758274 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/149 `/scratch/stefan/7898178/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=N[N-]N=N1) `REAL300019758274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758274 none CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 11, 7, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 1, 15, 16, 16, 16, 16, 15, 15, 15, 15, 13, 13, 11, 11, 11, 1, 1, 6, 1] 16 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758274 none CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 14, 14, 14, 16, 16, 16, 16] 16 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758274 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758274/1 /scratch/stefan/7898178/working/building/REAL300019758274 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/150 `/scratch/stefan/7898178/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=NN=N[N-]1) `REAL300019758274.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758274 none CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 11, 7, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 1, 15, 16, 16, 16, 16, 15, 15, 15, 15, 13, 13, 11, 11, 11, 1, 1, 6, 1] 16 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758274 none CC(CN(C)C(=O)C1=CC(Br)=CC(C=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 14, 14, 14, 16, 16, 16, 16] 16 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758274 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758274 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758274/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758274/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758274 Building REAL300019758275 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758275' /scratch/stefan/7898178/working/building/REAL300019758275 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758275 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758275/0 /scratch/stefan/7898178/working/building/REAL300019758275 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/151 `/scratch/stefan/7898178/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=NN=N[N-]1) `REAL300019758275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [72, 57, 34, 12, 34, 1, 12, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 72, 99, 99, 99, 99, 72, 72, 72, 72, 57, 57, 34, 34, 34, 1, 13, 13, 13, 13, 39] 603 rigid atoms, others: [33, 5, 7, 8, 9, 10, 17, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 402 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [185, 175, 130, 82, 130, 13, 82, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 185, 201, 201, 201, 201, 185, 185, 185, 185, 175, 175, 130, 130, 130, 13, 1, 1, 1, 1, 3] 603 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 681 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 516 conformations in input total number of sets (complete confs): 516 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 48, 48, 80, 80, 100, 100, 100, 172, 172, 172, 172, 172, 172, 100, 100, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 48, 48, 48, 100, 172, 172, 172, 172, 516] 516 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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: 1055 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758275 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758275/1 /scratch/stefan/7898178/working/building/REAL300019758275 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/152 `/scratch/stefan/7898178/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=N[N-]N=N1) `REAL300019758275.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [72, 57, 34, 12, 34, 1, 12, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 72, 100, 100, 100, 100, 72, 72, 72, 72, 57, 57, 34, 34, 34, 1, 13, 13, 13, 13, 39] 603 rigid atoms, others: [33, 5, 7, 8, 9, 10, 17, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 403 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [185, 175, 130, 82, 130, 13, 82, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 185, 201, 201, 201, 201, 185, 185, 185, 185, 175, 175, 130, 130, 130, 13, 1, 1, 1, 1, 3] 603 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 681 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758275 none CC(CN(C)C(=O)C1=CN([C@@H]2CC[C@H]2O)N=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 8, 5, 7, 5, 5, 5, 7, 12, 8, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 24, 46, 46, 80, 80, 99, 99, 99, 171, 171, 171, 171, 171, 171, 99, 99, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 46, 46, 46, 99, 171, 171, 171, 171, 513] 513 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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: 1051 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758275 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758275 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758275/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758275/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758275 Building REAL300019758276 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758276' /scratch/stefan/7898178/working/building/REAL300019758276 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758276 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758276/0 /scratch/stefan/7898178/working/building/REAL300019758276 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/153 `/scratch/stefan/7898178/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=NN=N[N-]1) `REAL300019758276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758276 none CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 11, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1] 4 rigid atoms, others: [33, 35, 36, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 13 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758276 none CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 11, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 16 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758276 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758276/1 /scratch/stefan/7898178/working/building/REAL300019758276 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/154 `/scratch/stefan/7898178/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=N[N-]N=N1) `REAL300019758276.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758276 none CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 11, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1] 4 rigid atoms, others: [33, 35, 36, 5, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 13 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758276 none CC(CN(C)C(=O)C1=CN2C(C=O)=CN=C2C(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 11, 1, 8, 1, 1, 17, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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]) total number of confs: 16 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758276 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758276 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758276/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758276/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758276 Building REAL300019758277 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758277' /scratch/stefan/7898178/working/building/REAL300019758277 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758277 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758277/0 /scratch/stefan/7898178/working/building/REAL300019758277 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/155 `/scratch/stefan/7898178/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=N[N-]N=N1) `REAL300019758277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 4, 5, 1, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 10, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 5, 5, 5, 3, 3, 2, 3, 3, 1, 1, 3, 1, 1] 36 rigid atoms, others: [5, 38, 7, 8, 41, 42, 39, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 4, 5, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 9, 3, 3] 36 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 36, 12, 12] 36 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758277 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758277/1 /scratch/stefan/7898178/working/building/REAL300019758277 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/156 `/scratch/stefan/7898178/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=NN=N[N-]1) `REAL300019758277.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 5, 4, 5, 1, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 5, 5, 5, 3, 3, 2, 3, 3, 1, 1, 3, 1, 1] 33 rigid atoms, others: [5, 38, 7, 8, 41, 42, 39, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 47 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 5, 4, 5, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 9, 3, 3] 33 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758277 none CC(CN(C)C(=O)[C@]1(C2=CC=CC=C2)C[C@H](O)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 1, 6, 8, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 33, 11, 11] 33 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758277 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758277 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758277/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758277/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758277 Building REAL300019758278 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758278' /scratch/stefan/7898178/working/building/REAL300019758278 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758278 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758278/0 /scratch/stefan/7898178/working/building/REAL300019758278 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/157 `/scratch/stefan/7898178/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=N[N-]N=N1) `REAL300019758278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=N[N-]N=N1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 17, 30, 30, 1, 16, 19, 19, 19, 19, 16, 16, 16, 16, 13, 13, 11, 11, 11, 6, 1, 1, 14, 14, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 46, 47, 21, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=N[N-]N=N1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 63, 54, 63, 30, 54, 30, 30, 30, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 30, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 63, 63, 63, 93, 30, 30, 3, 3, 1, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 280 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=N[N-]N=N1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 9, 12, 12, 15, 15, 19, 19, 19, 19, 31, 31, 31, 68, 68, 68, 68, 68, 68, 19, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 12, 12, 12, 57, 19, 19, 68, 68, 68, 68, 68, 68, 68, 19, 19] 204 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758278 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758278/1 /scratch/stefan/7898178/working/building/REAL300019758278 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/158 `/scratch/stefan/7898178/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=NN=N[N-]1) `REAL300019758278.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=NN=N[N-]1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 17, 30, 30, 1, 16, 19, 19, 19, 19, 16, 16, 16, 16, 13, 13, 11, 11, 11, 6, 1, 1, 14, 14, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 46, 47, 21, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=NN=N[N-]1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 63, 54, 63, 30, 54, 30, 30, 30, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 30, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 63, 63, 63, 93, 30, 30, 3, 3, 1, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 280 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758278 none CC(CN(C)C(=O)C1(O)CN(C(=O)OCC2=CC=CC=C2)C1)C1=NN=N[N-]1 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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 9, 12, 12, 15, 15, 19, 19, 19, 19, 31, 31, 31, 67, 67, 67, 67, 67, 67, 19, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 12, 12, 12, 57, 19, 19, 67, 67, 67, 67, 67, 67, 67, 19, 19] 201 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 318 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758278 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758278 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758278/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758278/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758278 Building REAL300019758279 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758279' /scratch/stefan/7898178/working/building/REAL300019758279 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758279 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758279/0 /scratch/stefan/7898178/working/building/REAL300019758279 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/159 `/scratch/stefan/7898178/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=N[N-]N=N1) `REAL300019758279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758279 none CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 6, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 39, 12, 13, 14, 15, 16, 17, 18, 41, 40, 37] set([0, 1, 2, 3, 4, 6, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758279 none CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 13, 16, 16, 18, 18, 18, 18, 19, 19, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 16, 16, 16, 19, 18, 18, 18, 18, 18, 18, 18, 18] 19 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758279 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758279/1 /scratch/stefan/7898178/working/building/REAL300019758279 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/160 `/scratch/stefan/7898178/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=NN=N[N-]1) `REAL300019758279.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758279 none CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 7, 7, 7, 7, 4, 4, 4, 4, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1] 8 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 39, 12, 13, 14, 15, 16, 17, 18, 41, 40, 37] set([0, 1, 2, 3, 4, 6, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758279 none CC(CN(C)C(=O)C1=C(C(F)F)N=C2CCCCN21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 5, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 13, 16, 16, 18, 18, 18, 18, 19, 19, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 16, 16, 16, 19, 18, 18, 18, 18, 18, 18, 18, 18] 19 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758279 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758279 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758279/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758279/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758279 Building REAL300019758280 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758280' /scratch/stefan/7898178/working/building/REAL300019758280 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758280 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758280/0 /scratch/stefan/7898178/working/building/REAL300019758280 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/161 `/scratch/stefan/7898178/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=NN=N[N-]1) `REAL300019758280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758280 none CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 9, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 34, 34, 34, 34, 31, 31, 31, 31, 25, 25, 9, 9, 9, 1, 1, 1, 1] 34 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758280 none CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 21, 21, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 21, 21, 21, 34, 34, 34, 34] 34 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758280 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758280/1 /scratch/stefan/7898178/working/building/REAL300019758280 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/162 `/scratch/stefan/7898178/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=N[N-]N=N1) `REAL300019758280.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758280 none CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 9, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 34, 34, 34, 34, 31, 31, 31, 31, 25, 25, 9, 9, 9, 1, 1, 1, 1] 34 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758280 none CC(CN(C)C(=O)C1=CN=C2SC=CC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 21, 21, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 21, 21, 21, 34, 34, 34, 34] 34 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758280 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758280 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758280/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758280/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758280 Building REAL300019758281 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758281' /scratch/stefan/7898178/working/building/REAL300019758281 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758281 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758281/0 /scratch/stefan/7898178/working/building/REAL300019758281 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/163 `/scratch/stefan/7898178/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC(F)(F)C(F)(F)F)C1=N[N-]N=N1) `REAL300019758281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758281 none CC(CN(C)C(=O)CC(F)(F)C(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 15, 15, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 27, 56, 56, 85, 85, 145, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 56, 56, 56, 145, 145] 201 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 888 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758281 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758281/1 /scratch/stefan/7898178/working/building/REAL300019758281 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/164 `/scratch/stefan/7898178/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC(F)(F)C(F)(F)F)C1=NN=N[N-]1) `REAL300019758281.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758281 none CC(CN(C)C(=O)CC(F)(F)C(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 15, 15, 5, 15, 15, 15, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 31, 60, 60, 89, 89, 146, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 12, 12, 12, 11, 31, 31, 60, 60, 60, 146, 146] 201 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 881 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758281 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758281 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758281/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758281/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758281 Building REAL300019758282 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758282' /scratch/stefan/7898178/working/building/REAL300019758282 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758282 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758282/0 /scratch/stefan/7898178/working/building/REAL300019758282 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/165 `/scratch/stefan/7898178/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=NN=N[N-]1) `REAL300019758282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758282 none CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 1, 8, 8, 8, 8, 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, 3, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 39, 39, 39, 39, 36, 36, 36, 36, 31, 31, 13, 13, 13, 1, 1, 1] 39 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758282 none CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 1, 8, 8, 8, 8, 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, 3, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 14, 24, 24, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 14, 24, 24, 24, 39, 39, 39] 39 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758282 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758282/1 /scratch/stefan/7898178/working/building/REAL300019758282 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/166 `/scratch/stefan/7898178/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=N[N-]N=N1) `REAL300019758282.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758282 none CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 1, 8, 8, 8, 8, 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, 3, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 39, 39, 39, 39, 36, 36, 36, 36, 31, 31, 13, 13, 13, 1, 1, 1] 39 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758282 none CC(CN(C)C(=O)C1=CC2=C(Cl)N=CC=C2O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 1, 8, 8, 8, 8, 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, 3, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 25, 25, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 25, 25, 25, 39, 39, 39] 39 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758282 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758282 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758282/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758282/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758282 Building REAL300019758283 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758283' /scratch/stefan/7898178/working/building/REAL300019758283 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758283 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758283/0 /scratch/stefan/7898178/working/building/REAL300019758283 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/167 `/scratch/stefan/7898178/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=N[N-]N=N1) `REAL300019758283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758283 none CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 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, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 122, 68, 122, 40, 68, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 122, 122, 122, 40, 40, 28, 28, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 876 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758283 none CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 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, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 25, 47, 47, 71, 71, 81, 105, 137, 137, 137, 145, 145, 145, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 47, 47, 47, 81, 81, 105, 105, 137, 145, 145, 145, 145, 145, 145] 145 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 548 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758283 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758283/1 /scratch/stefan/7898178/working/building/REAL300019758283 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/168 `/scratch/stefan/7898178/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=NN=N[N-]1) `REAL300019758283.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758283 none CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 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, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 122, 68, 122, 40, 68, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 122, 122, 122, 40, 40, 28, 28, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 876 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758283 none CC(CN(C)C(=O)CCNC(=O)C1=CC2=CC=CC=C2N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 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, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 27, 47, 47, 73, 73, 82, 105, 138, 138, 138, 146, 146, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 27, 47, 47, 47, 82, 82, 105, 105, 138, 146, 146, 146, 146, 146, 146] 146 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 545 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758283 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758283 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758283/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758283/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758283 Building REAL300019758284 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758284' /scratch/stefan/7898178/working/building/REAL300019758284 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758284 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758284/0 /scratch/stefan/7898178/working/building/REAL300019758284 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/169 `/scratch/stefan/7898178/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=NN=N[N-]1) `REAL300019758284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758284 none CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 32, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 40, 44, 44, 44, 44, 40, 40, 40, 40, 32, 32, 11, 11, 11, 1] 44 rigid atoms, others: [5, 7, 8, 9, 10, 11, 15, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758284 none CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 17, 28, 28, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 28, 28, 28, 44] 44 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758284 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758284/1 /scratch/stefan/7898178/working/building/REAL300019758284 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/170 `/scratch/stefan/7898178/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=N[N-]N=N1) `REAL300019758284.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758284 none CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 32, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 39, 43, 43, 43, 43, 39, 39, 39, 39, 32, 32, 11, 11, 11, 1] 43 rigid atoms, others: [5, 7, 8, 9, 10, 11, 15, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758284 none CC(CN(C)C(=O)C1=COC(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 17, 27, 27, 42, 42, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 27, 27, 27, 43] 43 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 155 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758284 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758284 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758284/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758284/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758284 Building REAL300019758285 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758285' /scratch/stefan/7898178/working/building/REAL300019758285 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758285 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758285/0 /scratch/stefan/7898178/working/building/REAL300019758285 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/171 `/scratch/stefan/7898178/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=NN=N[N-]1) `REAL300019758285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758285 none CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 8, 8, 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, 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: [29, 25, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 32, 32, 32, 32, 29, 29, 29, 29, 25, 25, 13, 13, 13, 1, 1, 1] 32 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758285 none CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 8, 8, 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, 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: [9, 1, 9, 13, 23, 23, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 23, 23, 23, 32, 32, 32] 32 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758285 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758285/1 /scratch/stefan/7898178/working/building/REAL300019758285 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/172 `/scratch/stefan/7898178/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=N[N-]N=N1) `REAL300019758285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758285 none CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 8, 8, 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, 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: [29, 25, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 32, 32, 32, 32, 29, 29, 29, 29, 25, 25, 13, 13, 13, 1, 1, 1] 32 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758285 none CC(CN(C)C(=O)C1=NN2C=C(Br)C=NC2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 8, 8, 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, 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: [9, 1, 9, 13, 23, 23, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 23, 23, 23, 32, 32, 32] 32 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758285 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758285 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758285/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758285/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758285 Building REAL300019758286 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758286' /scratch/stefan/7898178/working/building/REAL300019758286 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758286 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758286/0 /scratch/stefan/7898178/working/building/REAL300019758286 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/173 `/scratch/stefan/7898178/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758286 none COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 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, 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, 1, 1, 1, 1, 1, 5, 1, 1, 1, 6, 6, 10, 10, 13, 16, 16, 19, 19, 19, 19, 3, 3, 3, 1, 1, 5, 1, 10, 10, 10, 13, 13, 16, 16, 16, 16] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 10, 25, 26, 28] set([0, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758286 none COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 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, 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: [47, 42, 42, 42, 42, 42, 42, 47, 42, 34, 24, 34, 17, 24, 9, 1, 9, 1, 1, 1, 1, 1, 47, 47, 47, 42, 42, 47, 42, 24, 24, 24, 17, 17, 9, 9, 9, 9] 47 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758286 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758286/1 /scratch/stefan/7898178/working/building/REAL300019758286 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/174 `/scratch/stefan/7898178/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758286.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758286 none COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 5, 9, 9, 12, 14, 14, 17, 17, 17, 17, 3, 3, 3, 1, 1, 5, 1, 9, 9, 9, 12, 12, 14, 14, 14, 14] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 10, 25, 26, 28] set([0, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758286 none COC1=CC=C(C=O)C=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 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, 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: [47, 42, 42, 42, 42, 42, 42, 47, 42, 34, 24, 34, 17, 24, 9, 1, 9, 1, 1, 1, 1, 1, 47, 47, 47, 42, 42, 47, 42, 24, 24, 24, 17, 17, 9, 9, 9, 9] 47 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758286 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758286 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758286/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758286/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758286 Building REAL300019758287 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758287' /scratch/stefan/7898178/working/building/REAL300019758287 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758287 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758287/0 /scratch/stefan/7898178/working/building/REAL300019758287 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/175 `/scratch/stefan/7898178/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=N[N-]N=N1) `REAL300019758287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758287 none CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 14, 5, 11, 11, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 16, 15, 8, 15, 1, 8, 1, 1, 1, 1, 6, 6, 6, 1, 18, 19, 19, 19, 19, 18, 18, 18, 18, 16, 16, 15, 15, 15, 1, 1, 1, 7, 7, 7, 1, 1] 35 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758287 none CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 14, 5, 11, 11, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 26, 36, 36, 57, 57, 83, 83, 83, 131, 131, 131, 83, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 36, 36, 36, 83, 83, 83, 131, 131, 131, 83, 83] 131 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 551 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758287 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758287/1 /scratch/stefan/7898178/working/building/REAL300019758287 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/176 `/scratch/stefan/7898178/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=NN=N[N-]1) `REAL300019758287.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758287 none CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 14, 5, 11, 11, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 16, 15, 8, 15, 1, 8, 1, 1, 1, 1, 6, 6, 6, 1, 18, 19, 19, 19, 19, 18, 18, 18, 18, 16, 16, 15, 15, 15, 1, 1, 1, 7, 7, 7, 1, 1] 35 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758287 none CC(CN(C)C(=O)C1CN(S(C)(=O)=O)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 14, 5, 11, 11, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 26, 36, 36, 58, 58, 83, 83, 83, 131, 131, 131, 83, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 36, 36, 36, 83, 83, 83, 131, 131, 131, 83, 83] 131 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 553 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758287 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758287 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758287/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758287/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758287 Building REAL300019758288 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758288' /scratch/stefan/7898178/working/building/REAL300019758288 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758288 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758288/0 /scratch/stefan/7898178/working/building/REAL300019758288 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/177 `/scratch/stefan/7898178/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=N[N-]N=N1) `REAL300019758288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [27, 20, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 27, 43, 43, 43, 43, 27, 27, 27, 27, 20, 20, 13, 13, 13, 1, 1, 1, 2, 2, 2, 7, 7, 5, 7] 66 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [48, 44, 33, 16, 33, 7, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 48, 66, 66, 66, 66, 48, 48, 48, 48, 44, 44, 33, 33, 33, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 66 rigid atoms, others: [38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 16, 27, 27, 38, 38, 45, 45, 45, 45, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 27, 27, 27, 45, 45, 45, 45, 45, 45, 65, 65, 65, 65] 65 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 199 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758288 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758288/1 /scratch/stefan/7898178/working/building/REAL300019758288 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/178 `/scratch/stefan/7898178/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=NN=N[N-]1) `REAL300019758288.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [27, 20, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 27, 44, 44, 44, 44, 27, 27, 27, 27, 20, 20, 13, 13, 13, 1, 1, 1, 2, 2, 2, 7, 7, 5, 7] 67 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [48, 44, 33, 16, 33, 7, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 48, 67, 67, 67, 67, 48, 48, 48, 48, 44, 44, 33, 33, 33, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 67 rigid atoms, others: [38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 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: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758288 none CC(CN(C)C(=O)C1CC1(C)C1=CC=CC(Br)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 16, 27, 27, 38, 38, 45, 45, 45, 45, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 27, 27, 27, 45, 45, 45, 45, 45, 45, 66, 66, 66, 66] 66 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758288 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758288 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758288/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758288/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758288 Building REAL300019758289 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758289' /scratch/stefan/7898178/working/building/REAL300019758289 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758289 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758289/0 /scratch/stefan/7898178/working/building/REAL300019758289 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/179 `/scratch/stefan/7898178/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=NN=N[N-]1) `REAL300019758289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 50, 28, 10, 28, 1, 10, 1, 1, 1, 1, 1, 2, 7, 16, 16, 8, 16, 16, 1, 1, 80, 131, 131, 131, 131, 80, 80, 80, 80, 50, 50, 28, 28, 28, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 44, 19, 20] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 489 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 126, 58, 126, 16, 58, 16, 16, 16, 10, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 126, 126, 126, 16, 16, 3, 3, 1, 1, 1, 1, 1, 16] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 772 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 38, 38, 79, 79, 121, 121, 121, 121, 173, 201, 201, 201, 201, 201, 201, 121, 121, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 38, 38, 38, 121, 121, 201, 201, 201, 201, 201, 201, 201, 121] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44]) total number of confs: 571 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758289 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758289/1 /scratch/stefan/7898178/working/building/REAL300019758289 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/180 `/scratch/stefan/7898178/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=N[N-]N=N1) `REAL300019758289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 52, 28, 10, 28, 1, 10, 1, 1, 1, 1, 1, 2, 7, 16, 16, 8, 16, 16, 1, 1, 81, 129, 129, 129, 129, 81, 81, 81, 81, 52, 52, 28, 28, 28, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 44, 19, 20] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 489 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 125, 58, 125, 16, 58, 16, 16, 16, 10, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 125, 125, 125, 16, 16, 3, 3, 1, 1, 1, 1, 1, 16] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 779 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758289 none CC(CN(C)C(=O)C1=CC=C(OCC2=CC=CC=C2)C=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 24, 36, 36, 76, 76, 115, 115, 115, 115, 171, 201, 201, 201, 201, 201, 201, 115, 115, 1, 1, 1, 1, 1, 11, 11, 11, 11, 24, 24, 36, 36, 36, 115, 115, 201, 201, 201, 201, 201, 201, 201, 115] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44]) total number of confs: 573 number of broken/clashed sets: 42 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758289 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758289 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758289/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758289/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758289 Building REAL300019758290 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758290' /scratch/stefan/7898178/working/building/REAL300019758290 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758290 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758290/0 /scratch/stefan/7898178/working/building/REAL300019758290 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/181 `/scratch/stefan/7898178/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=N[N-]N=N1) `REAL300019758290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 23, 7, 23, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 55, 79, 79, 79, 79, 55, 55, 55, 55, 42, 42, 23, 23, 23, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19] 201 rigid atoms, others: [11, 5, 7, 8, 9, 10, 39, 12, 13, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48]) total number of confs: 311 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 141, 68, 141, 19, 68, 19, 19, 19, 19, 8, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 141, 141, 141, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [48, 13, 45, 14, 15, 16, 17, 18, 19, 20, 46, 22, 23, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 751 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 24, 38, 38, 57, 57, 79, 79, 79, 79, 79, 79, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 38, 38, 38, 79, 79, 79, 79, 140, 140, 201, 201, 201, 201] 201 rigid atoms, others: [1, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 666 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758290 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758290/1 /scratch/stefan/7898178/working/building/REAL300019758290 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/182 `/scratch/stefan/7898178/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=NN=N[N-]1) `REAL300019758290.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 23, 7, 23, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 55, 79, 79, 79, 79, 55, 55, 55, 55, 42, 42, 23, 23, 23, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19] 201 rigid atoms, others: [11, 5, 7, 8, 9, 10, 39, 12, 13, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48]) total number of confs: 311 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 142, 68, 142, 19, 68, 19, 19, 19, 19, 8, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 142, 142, 142, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [48, 13, 45, 14, 15, 16, 17, 18, 19, 20, 46, 22, 23, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 747 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758290 none CC(CN(C)C(=O)[C@H]1CC[C@@H](CN2C=NC3=C(N)N=CN=C32)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 39, 39, 58, 58, 80, 80, 80, 80, 80, 80, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 39, 39, 39, 80, 80, 80, 80, 141, 141, 201, 201, 201, 201] 201 rigid atoms, others: [1, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 664 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758290 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758290 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758290/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758290/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758290 Building REAL300019758291 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758291' /scratch/stefan/7898178/working/building/REAL300019758291 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758291 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758291/0 /scratch/stefan/7898178/working/building/REAL300019758291 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/183 `/scratch/stefan/7898178/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758291 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 1, 1, 1, 1, 7, 7, 19, 19, 40, 67, 67, 111, 111, 111, 111, 2, 2, 2, 25, 25, 25, 25, 1, 1, 19, 19, 19, 40, 40, 67, 67, 67, 67] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 34] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 453 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758291 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 158, 201, 201, 201, 201, 201, 116, 116, 85, 45, 85, 33, 45, 11, 1, 11, 1, 1, 1, 1, 1, 116, 116, 116, 201, 201, 201, 201, 116, 116, 45, 45, 45, 33, 33, 11, 11, 11, 11] 201 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758291 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758291/1 /scratch/stefan/7898178/working/building/REAL300019758291 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/184 `/scratch/stefan/7898178/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758291.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758291 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 1, 1, 1, 1, 7, 7, 19, 19, 40, 67, 67, 110, 110, 110, 110, 2, 2, 2, 25, 25, 25, 25, 1, 1, 19, 19, 19, 40, 40, 67, 67, 67, 67] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 34] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 452 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758291 none CC1=NC(OC(C)C(F)(F)F)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 12, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 159, 201, 201, 201, 201, 201, 115, 115, 84, 45, 84, 33, 45, 11, 1, 11, 1, 1, 1, 1, 1, 115, 115, 115, 201, 201, 201, 201, 115, 115, 45, 45, 45, 33, 33, 11, 11, 11, 11] 201 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758291 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758291 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758291/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758291/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758291 Building REAL300019758292 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758292' /scratch/stefan/7898178/working/building/REAL300019758292 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758292 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758292/0 /scratch/stefan/7898178/working/building/REAL300019758292 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/185 `/scratch/stefan/7898178/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)S2)=CS1) `REAL300019758292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 56, 56, 118, 118, 155, 167, 167, 201, 201, 201, 201, 13, 1, 1, 2, 2, 2, 13, 13, 118, 118, 118, 155, 155, 167, 167, 167, 167, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 674 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 61, 85, 85, 144, 144, 144, 144, 1, 12, 12, 13, 13, 13, 1, 1, 30, 30, 30, 61, 61, 85, 85, 85, 85, 13] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 119, 119, 119, 119, 77, 45, 77, 26, 45, 11, 1, 11, 1, 1, 1, 1, 1, 119, 145, 145, 145, 145, 145, 119, 119, 45, 45, 45, 26, 26, 11, 11, 11, 11, 145] 145 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758292 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758292/1 /scratch/stefan/7898178/working/building/REAL300019758292 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/186 `/scratch/stefan/7898178/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)S2)=CS1) `REAL300019758292.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 57, 57, 119, 119, 156, 168, 168, 201, 201, 201, 201, 13, 1, 1, 2, 2, 2, 13, 13, 119, 119, 119, 156, 156, 168, 168, 168, 168, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 674 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 61, 86, 86, 144, 144, 144, 144, 1, 12, 12, 13, 13, 13, 1, 1, 30, 30, 30, 61, 61, 86, 86, 86, 86, 13] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758292 none CC1=NC(C2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 119, 119, 119, 119, 77, 44, 77, 26, 44, 11, 1, 11, 1, 1, 1, 1, 1, 119, 146, 146, 146, 146, 146, 119, 119, 44, 44, 44, 26, 26, 11, 11, 11, 11, 146] 146 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758292 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758292 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758292/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758292/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758292 Building REAL300019758293 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758293' /scratch/stefan/7898178/working/building/REAL300019758293 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758293 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758293/0 /scratch/stefan/7898178/working/building/REAL300019758293 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/187 `/scratch/stefan/7898178/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=N[N-]N=N1) `REAL300019758293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [24, 20, 14, 12, 14, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 28, 28, 23, 28, 28, 24, 31, 31, 31, 31, 24, 24, 24, 24, 20, 20, 14, 14, 14, 5, 5, 1, 1, 1, 1, 16, 16, 28, 28, 28, 28] 59 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 57, 51, 49, 51, 35, 49, 28, 28, 28, 23, 28, 28, 13, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 57, 57, 51, 51, 51, 35, 35, 28, 24, 28, 28, 4, 4, 1, 1, 1, 1] 59 rigid atoms, others: [44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 10, 12, 12, 12, 12, 22, 27, 27, 27, 27, 27, 27, 31, 49, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 12, 12, 12, 22, 22, 27, 27, 27, 27, 49, 49, 52, 52, 52, 52] 52 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758293 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758293/1 /scratch/stefan/7898178/working/building/REAL300019758293 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/188 `/scratch/stefan/7898178/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=NN=N[N-]1) `REAL300019758293.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [24, 20, 14, 12, 14, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 28, 28, 23, 28, 28, 24, 31, 31, 31, 31, 24, 24, 24, 24, 20, 20, 14, 14, 14, 5, 5, 1, 1, 1, 1, 16, 16, 28, 28, 28, 28] 59 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 57, 51, 49, 51, 35, 49, 28, 28, 28, 23, 28, 28, 13, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 57, 57, 51, 51, 51, 35, 35, 28, 24, 28, 28, 4, 4, 1, 1, 1, 1] 59 rigid atoms, others: [44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758293 none CC(CN(C)C(=O)CC1=CC=CC=C1OCC1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 10, 12, 12, 12, 12, 22, 27, 27, 27, 27, 27, 27, 31, 49, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 12, 12, 12, 22, 22, 27, 27, 27, 27, 49, 49, 52, 52, 52, 52] 52 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758293 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758293 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758293/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758293/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758293 Building REAL300019758294 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758294' /scratch/stefan/7898178/working/building/REAL300019758294 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758294 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758294/0 /scratch/stefan/7898178/working/building/REAL300019758294 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/189 `/scratch/stefan/7898178/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=N[N-]N=N1) `REAL300019758294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 1, 31, 46, 46, 46, 46, 31, 31, 31, 31, 21, 21, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7] 58 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 20, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [56, 50, 17, 14, 17, 7, 14, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 56, 58, 58, 58, 58, 56, 56, 56, 56, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1] 58 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 224 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 20, 32, 32, 43, 43, 45, 45, 45, 45, 45, 45, 57, 57, 57, 57, 57, 57, 45, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 32, 32, 32, 45, 45, 45, 45, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 240 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758294 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758294/1 /scratch/stefan/7898178/working/building/REAL300019758294 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/190 `/scratch/stefan/7898178/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=NN=N[N-]1) `REAL300019758294.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [31, 21, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 1, 31, 47, 47, 47, 47, 31, 31, 31, 31, 21, 21, 6, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7] 58 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 20, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [56, 50, 17, 14, 17, 7, 14, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 56, 58, 58, 58, 58, 56, 56, 56, 56, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1] 58 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 224 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758294 none CC(CN(C)C(=O)[C@@H]1CC[C@H](CC2=CC=CC=C2)O1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 21, 33, 33, 44, 44, 46, 46, 46, 46, 46, 46, 57, 57, 57, 57, 57, 57, 46, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 33, 33, 33, 46, 46, 46, 46, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 240 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758294 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758294 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758294/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758294/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758294 Building REAL300019758295 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758295' /scratch/stefan/7898178/working/building/REAL300019758295 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758295 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758295/0 /scratch/stefan/7898178/working/building/REAL300019758295 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/191 `/scratch/stefan/7898178/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=N[N-]N=N1) `REAL300019758295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758295 none CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 64, 43, 20, 43, 6, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 64, 64, 43, 43, 43, 6, 6, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [43, 17, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 20, 21, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758295 none CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 20, 34, 34, 51, 51, 68, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 34, 34, 34, 68, 68, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 315 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758295 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758295/1 /scratch/stefan/7898178/working/building/REAL300019758295 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/192 `/scratch/stefan/7898178/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=NN=N[N-]1) `REAL300019758295.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758295 none CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 64, 43, 20, 43, 6, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 64, 64, 43, 43, 43, 6, 6, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [43, 17, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 20, 21, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758295 none CC(CN(C)C(=O)C[C@@H]1NC(=O)C2=CC=CC=C2NC1=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 19, 33, 33, 50, 50, 67, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 33, 33, 33, 67, 67, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [1, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 316 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758295 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758295 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758295/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758295/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758295 Building REAL300019758296 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758296' /scratch/stefan/7898178/working/building/REAL300019758296 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758296 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758296/0 /scratch/stefan/7898178/working/building/REAL300019758296 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/193 `/scratch/stefan/7898178/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=NN=N[N-]1) `REAL300019758296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [20, 14, 12, 7, 12, 1, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 20, 22, 22, 22, 22, 20, 20, 20, 20, 14, 14, 12, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 26 rigid atoms, others: [5, 7, 8, 41, 42, 43, 40, 18, 19] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [26, 20, 17, 11, 17, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 17, 17, 17, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 26 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [6, 1, 6, 10, 14, 14, 19, 19, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 22, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 14, 14, 14, 26, 26, 26, 26, 26, 26, 22, 22, 22, 22] 26 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758296 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758296/1 /scratch/stefan/7898178/working/building/REAL300019758296 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/194 `/scratch/stefan/7898178/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=N[N-]N=N1) `REAL300019758296.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [20, 14, 12, 7, 12, 1, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 20, 22, 22, 22, 22, 20, 20, 20, 20, 14, 14, 12, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 26 rigid atoms, others: [5, 7, 8, 41, 42, 43, 40, 18, 19] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [26, 20, 17, 11, 17, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 17, 17, 17, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 26 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758296 none CC(CN(C)C(=O)C1(C2=CC=NC3=CC=CC=C32)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [6, 1, 6, 10, 14, 14, 19, 19, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 22, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 14, 14, 14, 26, 26, 26, 26, 26, 26, 22, 22, 22, 22] 26 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758296 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758296 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758296/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758296/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758296 Building REAL300019758297 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758297' /scratch/stefan/7898178/working/building/REAL300019758297 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758297 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758297/0 /scratch/stefan/7898178/working/building/REAL300019758297 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/195 `/scratch/stefan/7898178/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=N[N-]N=N1) `REAL300019758297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 2, 3, 1, 2, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [5, 7, 8, 41, 42, 43, 44, 45, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 2, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 4 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 32 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758297 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758297/1 /scratch/stefan/7898178/working/building/REAL300019758297 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/196 `/scratch/stefan/7898178/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=NN=N[N-]1) `REAL300019758297.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 2, 3, 1, 2, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [5, 7, 8, 41, 42, 43, 44, 45, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 2, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 4 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758297 none CC(CN(C)C(=O)C1(C2CCCCO2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 32 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758297 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758297 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758297/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758297/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758297 Building REAL300019758298 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758298' /scratch/stefan/7898178/working/building/REAL300019758298 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758298 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758298/0 /scratch/stefan/7898178/working/building/REAL300019758298 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/197 `/scratch/stefan/7898178/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=N[N-]N=N1) `REAL300019758298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 16, 10, 6, 10, 1, 6, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 1, 1, 1, 23, 24, 24, 24, 24, 23, 23, 23, 23, 16, 16, 10, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [43, 5, 38, 7, 8, 41, 42, 17, 18, 19, 40, 39] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 19, 12, 8, 12, 4, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [7, 1, 7, 12, 17, 17, 19, 19, 24, 25, 25, 24, 24, 25, 25, 25, 25, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 17, 17, 17, 25, 25, 25, 25, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758298 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758298/1 /scratch/stefan/7898178/working/building/REAL300019758298 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/198 `/scratch/stefan/7898178/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=NN=N[N-]1) `REAL300019758298.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [23, 16, 10, 6, 10, 1, 6, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 1, 1, 1, 23, 24, 24, 24, 24, 23, 23, 23, 23, 16, 16, 10, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [43, 5, 38, 7, 8, 41, 42, 17, 18, 19, 40, 39] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 19, 12, 8, 12, 4, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758298 none CC(CN(C)C(=O)C1(C2=CC=C([N+](=O)[O-])C=C2)CCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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: [7, 1, 7, 12, 17, 17, 19, 19, 24, 25, 25, 24, 24, 25, 25, 25, 25, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 17, 17, 17, 25, 25, 25, 25, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758298 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758298 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758298/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758298/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758298 Building REAL300019758299 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758299' /scratch/stefan/7898178/working/building/REAL300019758299 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758299 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758299/0 /scratch/stefan/7898178/working/building/REAL300019758299 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/199 `/scratch/stefan/7898178/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=NN=N[N-]1) `REAL300019758299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758299 none CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 4, 3, 4, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1] 5 rigid atoms, others: [7, 40, 41, 10, 11, 12, 13, 14, 15, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 26 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758299 none CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758299 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758299/1 /scratch/stefan/7898178/working/building/REAL300019758299 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/200 `/scratch/stefan/7898178/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=N[N-]N=N1) `REAL300019758299.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758299 none CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 4, 3, 4, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1] 5 rigid atoms, others: [7, 40, 41, 10, 11, 12, 13, 14, 15, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 26 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758299 none CC(CN(C)C(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758299 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758299 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758299/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758299/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758299 Building REAL300019758300 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758300' /scratch/stefan/7898178/working/building/REAL300019758300 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758300 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758300/0 /scratch/stefan/7898178/working/building/REAL300019758300 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/201 `/scratch/stefan/7898178/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758300 none COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 6, 6, 21, 21, 52, 79, 79, 127, 127, 127, 127, 4, 4, 4, 1, 1, 6, 6, 6, 22, 22, 22, 52, 52, 79, 79, 79, 79] 131 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 26, 27] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758300 none COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 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, 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: [33, 32, 32, 32, 32, 32, 32, 32, 32, 33, 25, 21, 25, 16, 21, 9, 1, 9, 1, 1, 1, 1, 1, 33, 33, 33, 32, 32, 33, 33, 33, 21, 21, 21, 16, 16, 9, 9, 9, 9] 33 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758300 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758300/1 /scratch/stefan/7898178/working/building/REAL300019758300 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/202 `/scratch/stefan/7898178/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758300.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758300 none COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 6, 6, 21, 21, 52, 79, 79, 127, 127, 127, 127, 4, 4, 4, 1, 1, 6, 6, 6, 22, 22, 22, 52, 52, 79, 79, 79, 79] 131 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 26, 27] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758300 none COC1=CC=C(F)C(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 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, 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, 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: [33, 32, 32, 32, 32, 32, 32, 32, 32, 33, 26, 22, 26, 16, 22, 9, 1, 9, 1, 1, 1, 1, 1, 33, 33, 33, 32, 32, 33, 33, 33, 22, 22, 22, 16, 16, 9, 9, 9, 9] 33 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 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: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758300 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758300 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758300/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758300/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758300 Building REAL300019758301 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758301' /scratch/stefan/7898178/working/building/REAL300019758301 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758301 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758301/0 /scratch/stefan/7898178/working/building/REAL300019758301 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/203 `/scratch/stefan/7898178/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758301 none COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 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, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 20, 20, 24, 24, 24, 24, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 20, 20, 20, 20] 24 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758301 none COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 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, 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: [25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 15, 20, 9, 1, 9, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 15, 15, 9, 9, 9, 9] 25 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758301 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758301/1 /scratch/stefan/7898178/working/building/REAL300019758301 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/204 `/scratch/stefan/7898178/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758301.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758301 none COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 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, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 20, 20, 24, 24, 24, 24, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 20, 20, 20, 20] 24 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758301 none COC1=CC=NC(OC)=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 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, 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: [25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 15, 20, 9, 1, 9, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 15, 15, 9, 9, 9, 9] 25 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758301 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758301 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758301/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758301/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758301 Building REAL300019758302 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758302' /scratch/stefan/7898178/working/building/REAL300019758302 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758302 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758302/0 /scratch/stefan/7898178/working/building/REAL300019758302 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/205 `/scratch/stefan/7898178/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=N[N-]N=N1) `REAL300019758302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 16, 11, 5, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 11, 11, 10, 11, 11, 17, 18, 18, 18, 18, 17, 17, 17, 17, 16, 16, 11, 11, 11, 1, 1, 1, 1, 4, 4, 10, 10, 11, 11, 10, 11, 11] 35 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 24, 17, 9, 17, 4, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 17, 17, 17, 4, 4, 4, 4, 1, 1, 6, 6, 7, 7, 6, 7, 7] 35 rigid atoms, others: [12, 44, 45, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 18, 27, 11, 18, 11, 11, 11, 11, 11, 7, 11, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 11, 11, 11, 11, 7, 7, 4, 4, 1, 1, 1, 1, 1] 35 rigid atoms, others: [51, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 7, 9, 9, 15, 15, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 9, 9, 9, 19, 19, 19, 19, 26, 26, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [1, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758302 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758302/1 /scratch/stefan/7898178/working/building/REAL300019758302 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/206 `/scratch/stefan/7898178/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=NN=N[N-]1) `REAL300019758302.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 16, 11, 5, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 11, 11, 10, 11, 11, 17, 18, 18, 18, 18, 17, 17, 17, 17, 16, 16, 11, 11, 11, 1, 1, 1, 1, 4, 4, 10, 10, 11, 11, 10, 11, 11] 35 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 24, 17, 9, 17, 4, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 17, 17, 17, 4, 4, 4, 4, 1, 1, 6, 6, 7, 7, 6, 7, 7] 35 rigid atoms, others: [12, 44, 45, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 18, 27, 11, 18, 11, 11, 11, 11, 11, 7, 11, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 11, 11, 11, 11, 7, 7, 4, 4, 1, 1, 1, 1, 1] 35 rigid atoms, others: [51, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758302 none CC(CN(C)C(=O)[C@@H]1CCO[C@H]1C1=CC=NN1CC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 7, 9, 9, 15, 15, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 9, 9, 9, 19, 19, 19, 19, 26, 26, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [1, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758302 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758302 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758302/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758302/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758302 Building REAL300019758303 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758303' /scratch/stefan/7898178/working/building/REAL300019758303 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758303 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758303/0 /scratch/stefan/7898178/working/building/REAL300019758303 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/207 `/scratch/stefan/7898178/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1) `REAL300019758303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758303 none COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 47, 68, 68, 101, 101, 101, 101, 1, 8, 8, 8, 2, 2, 2, 27, 27, 27, 47, 47, 68, 68, 68, 68, 1] 126 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 367 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758303 none COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [114, 114, 93, 114, 93, 93, 93, 93, 69, 41, 69, 26, 41, 11, 1, 11, 1, 1, 1, 1, 1, 93, 114, 114, 114, 93, 93, 93, 41, 41, 41, 26, 26, 11, 11, 11, 11, 93] 114 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 382 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758303 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758303/1 /scratch/stefan/7898178/working/building/REAL300019758303 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/208 `/scratch/stefan/7898178/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1) `REAL300019758303.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758303 none COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 47, 68, 68, 101, 101, 101, 101, 1, 8, 8, 8, 2, 2, 2, 27, 27, 27, 47, 47, 68, 68, 68, 68, 1] 126 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 367 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758303 none COC(=O)C1=NN(C)C(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 94, 115, 94, 94, 94, 94, 72, 42, 72, 26, 42, 11, 1, 11, 1, 1, 1, 1, 1, 94, 115, 115, 115, 94, 94, 94, 42, 42, 42, 26, 26, 11, 11, 11, 11, 94] 115 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 387 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758303 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758303 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758303/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758303/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758303 Building REAL300019758304 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758304' /scratch/stefan/7898178/working/building/REAL300019758304 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758304 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758304/0 /scratch/stefan/7898178/working/building/REAL300019758304 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/209 `/scratch/stefan/7898178/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=N[N-]N=N2)C[C@H]1C) `REAL300019758304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758304 none COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=N[N-]N=N2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 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, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 29, 39, 39, 53, 53, 53, 53, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 29, 29, 39, 39, 39, 39, 1, 1, 2, 2, 2] 71 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758304 none COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=N[N-]N=N2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 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, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 53, 72, 53, 53, 53, 50, 53, 38, 50, 25, 38, 11, 1, 11, 1, 1, 1, 1, 1, 53, 53, 53, 53, 72, 72, 72, 38, 38, 38, 25, 25, 11, 11, 11, 11, 53, 53, 53, 53, 53] 72 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758304 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758304/1 /scratch/stefan/7898178/working/building/REAL300019758304 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/210 `/scratch/stefan/7898178/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=NN=N[N-]2)C[C@H]1C) `REAL300019758304.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758304 none COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=NN=N[N-]2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 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, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 29, 39, 39, 53, 53, 53, 53, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 29, 29, 39, 39, 39, 39, 1, 1, 2, 2, 2] 71 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758304 none COC(=O)[C@@H]1O[C@@H](C(=O)N(C)CC(C)C2=NN=N[N-]2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 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, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 53, 72, 53, 53, 53, 50, 53, 38, 50, 25, 38, 11, 1, 11, 1, 1, 1, 1, 1, 53, 53, 53, 53, 72, 72, 72, 38, 38, 38, 25, 25, 11, 11, 11, 11, 53, 53, 53, 53, 53] 72 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758304 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758304 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758304/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758304/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758304 Building REAL300019758305 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758305' /scratch/stefan/7898178/working/building/REAL300019758305 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758305 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758305/0 /scratch/stefan/7898178/working/building/REAL300019758305 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/211 `/scratch/stefan/7898178/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1) `REAL300019758305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 9, 9, 51, 52, 138, 136, 176, 201, 201, 201, 201, 201, 201, 18, 18, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 9, 18, 18, 138, 138, 138, 175, 175, 201, 201, 201, 201, 18, 18] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 777 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 10, 18, 18, 7, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 36, 52, 52, 77, 77, 77, 77, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 10, 18, 18, 7, 1, 1, 24, 24, 24, 36, 36, 52, 52, 52, 52, 1, 1] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 51, 52, 41, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 308 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 201, 201, 165, 73, 59, 73, 73, 35, 19, 35, 15, 19, 9, 1, 9, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 190, 201, 201, 165, 73, 73, 19, 19, 19, 15, 15, 9, 9, 9, 9, 73, 73] 201 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 613 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758305 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758305/1 /scratch/stefan/7898178/working/building/REAL300019758305 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/212 `/scratch/stefan/7898178/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1) `REAL300019758305.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 9, 9, 51, 52, 138, 136, 176, 201, 201, 201, 201, 201, 201, 18, 18, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 9, 18, 18, 138, 138, 138, 175, 175, 201, 201, 201, 201, 18, 18] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 777 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 10, 18, 18, 7, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 36, 52, 52, 77, 77, 77, 77, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 10, 18, 18, 7, 1, 1, 24, 24, 24, 36, 36, 52, 52, 52, 52, 1, 1] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 51, 52, 41, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 308 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758305 none CC(C)C1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 201, 201, 165, 73, 60, 73, 73, 36, 20, 36, 16, 20, 9, 1, 9, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 192, 201, 201, 165, 73, 73, 20, 20, 20, 16, 16, 9, 9, 9, 9, 73, 73] 201 rigid atoms, others: [19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 608 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758305 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758305 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758305/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758305/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758305 Building REAL300019758306 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758306' /scratch/stefan/7898178/working/building/REAL300019758306 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758306 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758306/0 /scratch/stefan/7898178/working/building/REAL300019758306 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/213 `/scratch/stefan/7898178/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1) `REAL300019758306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 12, 12, 57, 57, 117, 122, 156, 194, 194, 201, 201, 201, 201, 22, 22, 4, 4, 4, 1, 1, 1, 1, 10, 22, 22, 119, 117, 117, 156, 156, 194, 194, 194, 194, 22, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 22, 22, 22, 10, 22, 22, 7, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 32, 47, 47, 78, 78, 78, 78, 1, 1, 38, 38, 38, 22, 22, 22, 22, 7, 1, 1, 19, 19, 19, 32, 32, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 46, 47, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 200, 179, 200, 200, 154, 57, 37, 71, 71, 37, 26, 37, 21, 26, 10, 1, 10, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 200, 200, 153, 71, 71, 26, 26, 26, 21, 21, 10, 10, 10, 10, 71, 71] 201 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 765 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758306 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758306/1 /scratch/stefan/7898178/working/building/REAL300019758306 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/214 `/scratch/stefan/7898178/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1) `REAL300019758306.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 12, 12, 57, 57, 117, 122, 156, 194, 194, 201, 201, 201, 201, 22, 22, 4, 4, 4, 1, 1, 1, 1, 10, 22, 22, 119, 117, 117, 156, 156, 194, 194, 194, 194, 22, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 22, 22, 22, 10, 22, 22, 7, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 32, 47, 47, 78, 78, 78, 78, 1, 1, 38, 38, 38, 22, 22, 22, 22, 7, 1, 1, 19, 19, 19, 32, 32, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 46, 47, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758306 none COC1=CC=CC=C1NC1=CC=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 200, 180, 200, 200, 153, 56, 36, 69, 69, 36, 26, 36, 21, 26, 10, 1, 10, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 200, 200, 200, 153, 69, 69, 26, 26, 26, 21, 21, 10, 10, 10, 10, 69, 69] 201 rigid atoms, others: [18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 760 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758306 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758306 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758306/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758306/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758306 Building REAL300019758307 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758307' /scratch/stefan/7898178/working/building/REAL300019758307 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758307 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758307/0 /scratch/stefan/7898178/working/building/REAL300019758307 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/215 `/scratch/stefan/7898178/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2)C(OC)=C1) `REAL300019758307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 10, 10, 6, 7, 33, 33, 57, 57, 87, 135, 135, 173, 173, 173, 173, 10, 10, 1, 1, 4, 1, 3, 3, 3, 1, 1, 6, 10, 10, 57, 57, 57, 87, 87, 135, 135, 135, 135, 10, 10, 4, 4, 4, 1] 196 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 51, 25, 26, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 735 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 15, 29, 29, 70, 70, 70, 70, 1, 1, 10, 10, 18, 10, 16, 16, 16, 10, 10, 6, 1, 1, 9, 9, 9, 15, 15, 29, 29, 29, 29, 1, 1, 18, 18, 18, 10] 196 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=N[N-]N=N3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 145, 145, 145, 145, 129, 51, 51, 51, 51, 32, 32, 32, 18, 32, 12, 1, 12, 1, 1, 1, 1, 1, 51, 51, 145, 145, 171, 145, 171, 171, 171, 145, 145, 129, 51, 51, 32, 32, 32, 18, 18, 12, 12, 12, 12, 51, 51, 171, 171, 171, 145] 171 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 508 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758307 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758307/1 /scratch/stefan/7898178/working/building/REAL300019758307 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/216 `/scratch/stefan/7898178/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2)C(OC)=C1) `REAL300019758307.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 10, 10, 6, 7, 33, 33, 57, 57, 87, 133, 133, 172, 172, 172, 172, 10, 10, 1, 1, 4, 1, 3, 3, 3, 1, 1, 6, 10, 10, 57, 57, 57, 87, 87, 133, 133, 133, 133, 10, 10, 4, 4, 4, 1] 197 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 51, 25, 26, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 725 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 15, 29, 29, 68, 68, 68, 68, 1, 1, 10, 10, 18, 10, 16, 16, 16, 10, 10, 6, 1, 1, 9, 9, 9, 15, 15, 29, 29, 29, 29, 1, 1, 18, 18, 18, 10] 197 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758307 none COC1=CC=C(NC2=CC=C(C(=O)N(C)CC(C)C3=NN=N[N-]3)C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 146, 146, 146, 146, 130, 50, 50, 50, 50, 31, 31, 31, 17, 31, 11, 1, 11, 1, 1, 1, 1, 1, 50, 50, 146, 146, 173, 146, 173, 173, 173, 146, 146, 130, 50, 50, 31, 31, 31, 17, 17, 11, 11, 11, 11, 50, 50, 173, 173, 173, 146] 173 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 515 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758307 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758307 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758307/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758307/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758307 Building REAL300019758308 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758308' /scratch/stefan/7898178/working/building/REAL300019758308 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758308 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758308/0 /scratch/stefan/7898178/working/building/REAL300019758308 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/217 `/scratch/stefan/7898178/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=N[N-]N=N1) `REAL300019758308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 13, 18, 18, 13, 18, 18, 18, 18, 18, 18, 1, 1, 41, 68, 68, 68, 68, 41, 41, 41, 41, 26, 26, 15, 15, 15, 1, 1, 13, 18, 18, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 22, 23, 55, 54] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 277 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 155, 103, 40, 103, 10, 40, 10, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 195, 201, 201, 201, 201, 195, 195, 195, 195, 155, 155, 103, 103, 103, 18, 18, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 846 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 23, 33, 33, 52, 52, 68, 68, 53, 53, 190, 201, 201, 192, 201, 201, 201, 201, 201, 201, 68, 68, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 33, 33, 33, 68, 68, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68] 201 rigid atoms, others: [1, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 668 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758308 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758308/1 /scratch/stefan/7898178/working/building/REAL300019758308 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/218 `/scratch/stefan/7898178/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=NN=N[N-]1) `REAL300019758308.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 13, 18, 18, 13, 18, 18, 18, 18, 18, 18, 1, 1, 41, 68, 68, 68, 68, 41, 41, 41, 41, 26, 26, 15, 15, 15, 1, 1, 13, 18, 18, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 22, 23, 55, 54] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 277 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 155, 103, 40, 103, 10, 40, 10, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 195, 201, 201, 201, 201, 195, 195, 195, 195, 155, 155, 103, 103, 103, 18, 18, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 846 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758308 none CC(CN(C)C(=O)C1=CC=C(NC2=CC=CC=C2C(C)(C)C)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 23, 33, 33, 53, 53, 69, 69, 54, 54, 190, 201, 201, 191, 201, 201, 201, 201, 201, 201, 69, 69, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 33, 33, 33, 69, 69, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69] 201 rigid atoms, others: [1, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 673 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758308 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758308 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758308/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758308/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758308 Building REAL300019758309 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758309' /scratch/stefan/7898178/working/building/REAL300019758309 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758309 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758309/0 /scratch/stefan/7898178/working/building/REAL300019758309 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/219 `/scratch/stefan/7898178/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=N[N-]N=N1) `REAL300019758309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758309 none CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 169, 123, 72, 123, 12, 72, 12, 1, 1, 1, 1, 1, 1, 1, 181, 201, 201, 201, 201, 181, 181, 181, 181, 169, 169, 125, 125, 125, 12, 12, 1, 1] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 713 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758309 none CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 28, 40, 40, 64, 64, 91, 91, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 28, 40, 40, 40, 91, 91, 119, 119] 119 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 393 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758309 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758309/1 /scratch/stefan/7898178/working/building/REAL300019758309 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/220 `/scratch/stefan/7898178/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=NN=N[N-]1) `REAL300019758309.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758309 none CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 169, 122, 72, 122, 12, 72, 12, 1, 1, 1, 1, 1, 1, 1, 182, 201, 201, 201, 201, 182, 182, 182, 182, 169, 169, 124, 124, 124, 12, 12, 1, 1] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 713 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758309 none CC(CN(C)C(=O)C=CC1=CC=C(Cl)S1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 29, 41, 41, 66, 66, 92, 92, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 12, 12, 12, 12, 29, 29, 41, 41, 41, 92, 92, 119, 119] 119 rigid atoms, others: [1, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 392 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758309 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758309 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758309/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758309/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758309 Building REAL300019758310 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758310' /scratch/stefan/7898178/working/building/REAL300019758310 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758310 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758310/0 /scratch/stefan/7898178/working/building/REAL300019758310 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/221 `/scratch/stefan/7898178/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=N[N-]N=N1) `REAL300019758310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758310 none CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 67, 40, 24, 39, 9, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 107, 178, 178, 178, 178, 107, 107, 107, 107, 67, 67, 40, 40, 40, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 642 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758310 none CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 29, 55, 55, 73, 73, 117, 117, 171, 171, 129, 171, 171, 171, 199, 199, 199, 199, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 55, 55, 55, 117, 117, 171, 171, 171, 171] 199 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39]) total number of confs: 735 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758310 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758310/1 /scratch/stefan/7898178/working/building/REAL300019758310 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/222 `/scratch/stefan/7898178/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=NN=N[N-]1) `REAL300019758310.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758310 none CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 67, 40, 24, 39, 9, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 107, 178, 178, 178, 178, 107, 107, 107, 107, 67, 67, 40, 40, 40, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 643 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758310 none CC(CN(C)C(=O)C=CC1=CC=CC=C1OC(F)(F)F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 8, 8, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 29, 55, 55, 73, 73, 119, 119, 173, 173, 131, 173, 173, 173, 201, 201, 201, 201, 1, 1, 1, 1, 1, 12, 12, 12, 12, 29, 29, 55, 55, 55, 119, 119, 173, 173, 173, 173] 201 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39]) total number of confs: 738 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758310 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758310 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758310/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758310/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758310 Building REAL300019758311 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758311' /scratch/stefan/7898178/working/building/REAL300019758311 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758311 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758311/0 /scratch/stefan/7898178/working/building/REAL300019758311 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/223 `/scratch/stefan/7898178/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=NN=N[N-]1) `REAL300019758311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 52, 30, 11, 30, 1, 11, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 70, 113, 113, 113, 113, 70, 70, 70, 70, 52, 52, 30, 30, 30, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 16, 17, 41, 42] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 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: 383 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 155, 123, 77, 123, 13, 77, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 170, 201, 201, 201, 201, 170, 170, 170, 170, 155, 155, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 651 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 20, 35, 35, 54, 54, 56, 56, 56, 97, 97, 97, 97, 97, 56, 56, 1, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 35, 35, 35, 97, 97, 97, 97, 97, 97, 97, 97, 97, 56, 56] 97 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 329 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758311 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758311/1 /scratch/stefan/7898178/working/building/REAL300019758311 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/224 `/scratch/stefan/7898178/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=N[N-]N=N1) `REAL300019758311.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 52, 30, 11, 30, 1, 11, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 70, 113, 113, 113, 113, 70, 70, 70, 70, 52, 52, 30, 30, 30, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 16, 17, 41, 42] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 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: 383 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 155, 123, 77, 123, 13, 77, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 170, 201, 201, 201, 201, 170, 170, 170, 170, 155, 155, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 651 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758311 none CC(CN(C)C(=O)C1=NN(C2CCOCC2)C=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 20, 34, 34, 51, 51, 54, 54, 54, 95, 95, 95, 95, 95, 54, 54, 1, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 34, 34, 34, 95, 95, 95, 95, 95, 95, 95, 95, 95, 54, 54] 95 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 319 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758311 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758311 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758311/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758311/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758311 Building REAL300019758312 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758312' /scratch/stefan/7898178/working/building/REAL300019758312 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758312 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758312/0 /scratch/stefan/7898178/working/building/REAL300019758312 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/225 `/scratch/stefan/7898178/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=N[N-]N=N1) `REAL300019758312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758312 none CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [15, 14, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 17, 17, 15, 15, 15, 15, 14, 14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758312 none CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 1, 7, 9, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758312 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758312/1 /scratch/stefan/7898178/working/building/REAL300019758312 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/226 `/scratch/stefan/7898178/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=NN=N[N-]1) `REAL300019758312.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758312 none CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [15, 14, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 17, 17, 15, 15, 15, 15, 14, 14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758312 none CC(CN(C)C(=O)[C@@]12CC[C@@](C)(C(=O)O1)C2(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 1, 7, 9, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758312 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758312 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758312/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758312/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758312 Building REAL300019758313 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758313' /scratch/stefan/7898178/working/building/REAL300019758313 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758313 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758313/0 /scratch/stefan/7898178/working/building/REAL300019758313 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/227 `/scratch/stefan/7898178/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=N[N-]N=N1) `REAL300019758313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758313 none CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 24, 10, 7, 10, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 32, 32, 32, 32, 28, 28, 28, 28, 24, 24, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758313 none CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 12, 15, 15, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758313 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758313/1 /scratch/stefan/7898178/working/building/REAL300019758313 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/228 `/scratch/stefan/7898178/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=NN=N[N-]1) `REAL300019758313.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758313 none CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 24, 10, 7, 10, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 32, 32, 32, 32, 28, 28, 28, 28, 24, 24, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758313 none CC(CN(C)C(=O)C1C2CC3=C(Br)C=CC=C3C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 12, 15, 15, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758313 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758313 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758313/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758313/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758313 Building REAL300019758314 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758314' /scratch/stefan/7898178/working/building/REAL300019758314 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758314 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758314/0 /scratch/stefan/7898178/working/building/REAL300019758314 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/229 `/scratch/stefan/7898178/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C(C2=CC=CC=C2)O1) `REAL300019758314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 33, 33, 57, 90, 90, 167, 167, 167, 167, 1, 1, 1, 7, 7, 2, 7, 7, 1, 2, 2, 2, 33, 33, 33, 57, 57, 90, 90, 90, 90, 1, 7, 7, 7, 7, 7] 172 rigid atoms, others: [0, 1, 2, 3, 36, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 536 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 90, 46, 90, 25, 46, 10, 1, 10, 1, 1, 1, 1, 1, 134, 134, 134, 139, 139, 139, 139, 139, 134, 134, 134, 134, 46, 46, 46, 25, 25, 10, 10, 10, 10, 134, 139, 139, 139, 139, 139] 139 rigid atoms, others: [8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 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: 399 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 33, 33, 97, 97, 133, 158, 158, 172, 172, 172, 172, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 97, 97, 97, 133, 133, 158, 158, 158, 158, 7, 1, 1, 1, 1, 1] 172 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 610 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758314 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758314/1 /scratch/stefan/7898178/working/building/REAL300019758314 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/230 `/scratch/stefan/7898178/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C(C2=CC=CC=C2)O1) `REAL300019758314.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 33, 33, 57, 90, 90, 168, 168, 168, 168, 1, 1, 1, 7, 7, 2, 7, 7, 1, 2, 2, 2, 33, 33, 33, 57, 57, 90, 90, 90, 90, 1, 7, 7, 7, 7, 7] 173 rigid atoms, others: [0, 1, 2, 3, 36, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 535 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 92, 47, 92, 25, 47, 10, 1, 10, 1, 1, 1, 1, 1, 134, 134, 134, 139, 139, 139, 139, 139, 134, 134, 134, 134, 47, 47, 47, 25, 25, 10, 10, 10, 10, 134, 139, 139, 139, 139, 139] 139 rigid atoms, others: [8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 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: 400 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758314 none CC1=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 32, 32, 95, 95, 130, 156, 156, 173, 173, 173, 173, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 95, 95, 95, 130, 130, 156, 156, 156, 156, 7, 1, 1, 1, 1, 1] 173 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 613 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758314 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758314 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758314/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758314/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758314 Building REAL300019758315 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758315' /scratch/stefan/7898178/working/building/REAL300019758315 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758315 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758315/0 /scratch/stefan/7898178/working/building/REAL300019758315 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/231 `/scratch/stefan/7898178/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=N[N-]N=N1) `REAL300019758315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758315 none CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758315 none CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 13, 15, 15, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758315 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758315/1 /scratch/stefan/7898178/working/building/REAL300019758315 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/232 `/scratch/stefan/7898178/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=NN=N[N-]1) `REAL300019758315.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758315 none CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758315 none CC(CN(C)C(=O)C1CNC(=O)C2=CC=CC=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 13, 15, 15, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758315 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758315 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758315/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758315/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758315 Building REAL300019758316 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758316' /scratch/stefan/7898178/working/building/REAL300019758316 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758316 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758316/0 /scratch/stefan/7898178/working/building/REAL300019758316 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/233 `/scratch/stefan/7898178/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=N[N-]N=N1) `REAL300019758316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758316 none CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 133, 73, 28, 73, 8, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 201, 201, 201, 201, 163, 163, 163, 163, 133, 133, 73, 73, 73, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 743 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758316 none CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 17, 17, 25, 25, 27, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 17, 17, 17, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758316 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758316/1 /scratch/stefan/7898178/working/building/REAL300019758316 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/234 `/scratch/stefan/7898178/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=NN=N[N-]1) `REAL300019758316.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758316 none CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 135, 73, 28, 73, 8, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 201, 165, 165, 165, 165, 135, 135, 73, 73, 73, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 751 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758316 none CC(CN(C)C(=O)CC1CCC(F)(F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 17, 17, 25, 25, 27, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 17, 17, 17, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [1, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758316 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758316 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758316/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758316/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758316 Building REAL300019758317 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758317' /scratch/stefan/7898178/working/building/REAL300019758317 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758317 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758317/0 /scratch/stefan/7898178/working/building/REAL300019758317 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/235 `/scratch/stefan/7898178/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)N=C1C(F)(F)F) `REAL300019758317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758317 none CC1=CN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 40, 40, 102, 102, 155, 184, 184, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 9, 102, 102, 102, 155, 155, 184, 184, 184, 184] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 775 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758317 none CC1=CN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 79, 46, 79, 24, 46, 11, 1, 11, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 46, 46, 46, 24, 24, 11, 11, 11, 11] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 667 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758317 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758317/1 /scratch/stefan/7898178/working/building/REAL300019758317 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/236 `/scratch/stefan/7898178/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)N=C1C(F)(F)F) `REAL300019758317.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758317 none CC1=CN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 40, 40, 103, 103, 157, 184, 184, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 9, 103, 103, 103, 157, 157, 184, 184, 184, 184] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 768 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758317 none CC1=CN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 78, 45, 78, 24, 45, 11, 1, 11, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 45, 45, 45, 24, 24, 11, 11, 11, 11] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 670 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758317 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758317 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758317/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758317/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758317 Building REAL300019758318 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758318' /scratch/stefan/7898178/working/building/REAL300019758318 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758318 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758318/0 /scratch/stefan/7898178/working/building/REAL300019758318 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/237 `/scratch/stefan/7898178/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H](CO)NC(=O)OC(C)(C)C)C1=N[N-]N=N1) `REAL300019758318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758318 none CC(CN(C)C(=O)[C@@H](CO)NC(=O)OC(C)(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 7, 8, 8, 9, 9, 12, 12, 15, 12, 14, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 15, 15, 45, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17] 54 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758318 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758318/1 /scratch/stefan/7898178/working/building/REAL300019758318 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/238 `/scratch/stefan/7898178/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)[C@@H](CO)NC(=O)OC(C)(C)C)C1=NN=N[N-]1) `REAL300019758318.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758318 none CC(CN(C)C(=O)[C@@H](CO)NC(=O)OC(C)(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 7, 8, 8, 9, 9, 12, 12, 15, 12, 14, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 15, 15, 45, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17] 54 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758318 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758318 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758318/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758318/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758318 Building REAL300019758319 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758319' /scratch/stefan/7898178/working/building/REAL300019758319 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758319 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758319/0 /scratch/stefan/7898178/working/building/REAL300019758319 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/239 `/scratch/stefan/7898178/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1) `REAL300019758319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758319 none COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 528 conformations in input total number of sets (complete confs): 528 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 1, 1, 1, 1, 7, 7, 25, 25, 43, 73, 73, 125, 125, 125, 125, 3, 3, 3, 1, 9, 9, 27, 1, 1, 25, 25, 25, 43, 43, 73, 73, 73, 73] 528 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 25, 29, 30] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 457 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758319 none COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [47, 43, 43, 43, 43, 43, 56, 43, 43, 34, 30, 34, 22, 30, 11, 1, 11, 1, 1, 1, 1, 1, 47, 47, 47, 43, 56, 56, 168, 43, 43, 30, 30, 30, 22, 22, 11, 11, 11, 11] 168 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 404 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758319 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758319/1 /scratch/stefan/7898178/working/building/REAL300019758319 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/240 `/scratch/stefan/7898178/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1) `REAL300019758319.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758319 none COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 534 conformations in input total number of sets (complete confs): 534 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 1, 1, 1, 1, 7, 7, 25, 25, 43, 73, 73, 126, 126, 126, 126, 3, 3, 3, 1, 9, 9, 27, 1, 1, 25, 25, 25, 43, 43, 73, 73, 73, 73] 534 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 25, 29, 30] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 459 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758319 none COC1=CC(CO)=CC=C1C(=O)N(C)CC(C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [47, 43, 43, 43, 43, 43, 56, 43, 43, 35, 32, 35, 22, 32, 11, 1, 11, 1, 1, 1, 1, 1, 47, 47, 47, 43, 56, 56, 168, 43, 43, 32, 32, 32, 22, 22, 11, 11, 11, 11] 168 rigid atoms, others: [15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 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: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758319 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758319 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758319/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758319/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758319 Building REAL300019758320 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758320' /scratch/stefan/7898178/working/building/REAL300019758320 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758320 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758320/0 /scratch/stefan/7898178/working/building/REAL300019758320 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/241 `/scratch/stefan/7898178/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=N[N-]N=N1) `REAL300019758320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758320 none CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 60, 38, 14, 38, 5, 14, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 78, 124, 124, 124, 124, 78, 78, 78, 78, 60, 60, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 7, 7, 12, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 16, 17, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 435 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758320 none CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 52, 52, 80, 80, 90, 123, 123, 123, 123, 172, 172, 172, 123, 123, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 52, 52, 52, 90, 90, 123, 123, 123, 123, 123, 172, 172, 172, 123, 123, 123, 123] 172 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 752 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758320 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758320/1 /scratch/stefan/7898178/working/building/REAL300019758320 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/242 `/scratch/stefan/7898178/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=NN=N[N-]1) `REAL300019758320.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758320 none CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 60, 38, 14, 38, 5, 14, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 78, 124, 124, 124, 124, 78, 78, 78, 78, 60, 60, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 7, 7, 12, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 16, 17, 43, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 435 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758320 none CC(CN(C)C(=O)CC1CCN(CC(F)F)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 25, 52, 52, 80, 80, 90, 123, 123, 123, 123, 172, 172, 172, 123, 123, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 52, 52, 52, 90, 90, 123, 123, 123, 123, 123, 172, 172, 172, 123, 123, 123, 123] 172 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 752 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758320 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758320 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758320/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758320/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758320 Building REAL300019758321 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758321' /scratch/stefan/7898178/working/building/REAL300019758321 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758321 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758321/0 /scratch/stefan/7898178/working/building/REAL300019758321 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/243 `/scratch/stefan/7898178/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1C=O) `REAL300019758321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758321 none COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 22, 22, 35, 54, 54, 95, 95, 95, 95, 1, 1, 1, 3, 4, 4, 4, 1, 4, 4, 4, 22, 22, 22, 35, 35, 54, 54, 54, 54, 1, 3] 99 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 40, 20, 21, 22, 27] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758321 none COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=N[N-]N=N2)C=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 69, 69, 69, 69, 69, 70, 47, 32, 47, 21, 32, 10, 1, 10, 1, 1, 1, 1, 1, 69, 69, 69, 69, 70, 70, 70, 69, 70, 70, 70, 32, 32, 32, 21, 21, 10, 10, 10, 10, 69, 69] 70 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 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: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758321 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758321/1 /scratch/stefan/7898178/working/building/REAL300019758321 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/244 `/scratch/stefan/7898178/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1C=O) `REAL300019758321.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758321 none COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 22, 22, 33, 53, 53, 97, 97, 97, 97, 1, 1, 1, 3, 4, 4, 4, 1, 4, 4, 4, 22, 22, 22, 33, 33, 53, 53, 53, 53, 1, 3] 101 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 40, 20, 21, 22, 27] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758321 none COC1=CC(OC)=C(C(=O)N(C)CC(C)C2=NN=N[N-]2)C=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 70, 70, 70, 70, 70, 72, 49, 31, 49, 21, 31, 10, 1, 10, 1, 1, 1, 1, 1, 70, 70, 70, 71, 72, 72, 72, 70, 72, 72, 72, 31, 31, 31, 21, 21, 10, 10, 10, 10, 70, 71] 72 rigid atoms, others: [13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 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: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758321 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758321 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758321/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758321/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758321 Building REAL300019758322 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758322' /scratch/stefan/7898178/working/building/REAL300019758322 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758322 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758322/0 /scratch/stefan/7898178/working/building/REAL300019758322 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/245 `/scratch/stefan/7898178/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1) `REAL300019758322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758322 none CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 59, 47, 59, 26, 47, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 59, 59, 59, 26, 26, 14, 14, 8, 8, 1, 2, 2, 1] 76 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 310 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758322 none CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 8, 11, 11, 14, 14, 26, 33, 41, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 11, 11, 11, 26, 26, 36, 36, 40, 41, 72, 72, 72, 72] 72 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758322 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758322/1 /scratch/stefan/7898178/working/building/REAL300019758322 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/246 `/scratch/stefan/7898178/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1) `REAL300019758322.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758322 none CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 59, 47, 59, 26, 47, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 59, 59, 59, 26, 26, 14, 14, 8, 8, 1, 2, 2, 1] 76 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 310 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758322 none CC(CN(C)C(=O)CCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 8, 11, 11, 14, 14, 26, 33, 41, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 11, 11, 11, 26, 26, 36, 36, 40, 41, 72, 72, 72, 72] 72 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758322 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758322 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758322/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758322/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758322 Building REAL300019758323 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758323' /scratch/stefan/7898178/working/building/REAL300019758323 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758323 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758323/0 /scratch/stefan/7898178/working/building/REAL300019758323 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/247 `/scratch/stefan/7898178/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1) `REAL300019758323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758323 none CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 121, 72, 121, 34, 72, 21, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 121, 121, 121, 34, 34, 21, 21, 16, 16, 8, 8, 1, 2, 2, 1] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 894 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758323 none CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 20, 41, 41, 66, 66, 80, 86, 95, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 41, 41, 41, 80, 80, 87, 87, 95, 95, 112, 112, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46]) total number of confs: 606 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758323 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758323/1 /scratch/stefan/7898178/working/building/REAL300019758323 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/248 `/scratch/stefan/7898178/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1) `REAL300019758323.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758323 none CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 121, 72, 121, 34, 72, 21, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 121, 121, 121, 34, 34, 21, 21, 16, 16, 8, 8, 1, 2, 2, 1] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 894 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758323 none CC(CN(C)C(=O)CCCCN1C=NC2=C(N)N=CN=C21)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 8, 1, 1, 8, 8, 1, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 20, 41, 41, 66, 66, 80, 86, 95, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 41, 41, 41, 80, 80, 87, 87, 95, 95, 114, 114, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45, 46]) total number of confs: 616 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758323 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758323 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758323/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758323/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758323 Building REAL300019758324 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758324' /scratch/stefan/7898178/working/building/REAL300019758324 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758324 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758324/0 /scratch/stefan/7898178/working/building/REAL300019758324 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/249 `/scratch/stefan/7898178/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=N[N-]N=N1) `REAL300019758324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758324 none CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 71, 71, 71, 59, 71, 45, 35, 45, 13, 4, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 71, 71, 71, 59, 59, 45, 135, 35, 35, 4, 4, 1, 1, 1, 1, 1] 246 rigid atoms, others: [45, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 503 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758324 none CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 10, 12, 12, 12, 12, 18, 27, 27, 35, 47, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 12, 12, 12, 18, 18, 27, 81, 35, 35, 72, 72, 72, 72, 72, 72, 72] 216 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 382 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758324 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758324/1 /scratch/stefan/7898178/working/building/REAL300019758324 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/250 `/scratch/stefan/7898178/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=NN=N[N-]1) `REAL300019758324.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758324 none CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 71, 71, 71, 59, 71, 45, 35, 45, 13, 4, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 71, 71, 71, 59, 59, 45, 135, 35, 35, 4, 4, 1, 1, 1, 1, 1] 246 rigid atoms, others: [45, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 503 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758324 none CC(CN(C)C(=O)CC(O)COCC1=CC=CC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 10, 12, 12, 12, 12, 18, 27, 27, 35, 47, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 12, 12, 12, 18, 18, 27, 81, 35, 35, 72, 72, 72, 72, 72, 72, 72] 216 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 382 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758324 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758324 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758324/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758324/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758324 Building REAL300019758325 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758325' /scratch/stefan/7898178/working/building/REAL300019758325 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758325 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758325/0 /scratch/stefan/7898178/working/building/REAL300019758325 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/251 `/scratch/stefan/7898178/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=N[N-]N=N1) `REAL300019758325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [58, 38, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 13, 13, 6, 13, 13, 13, 1, 58, 91, 91, 91, 91, 58, 58, 58, 58, 38, 38, 18, 18, 18, 1, 1, 1, 6, 13, 13, 12, 13, 1, 1] 594 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 347 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [179, 155, 89, 38, 89, 13, 38, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 13, 179, 198, 198, 198, 198, 179, 179, 179, 179, 155, 155, 89, 89, 89, 13, 13, 13, 39, 1, 1, 1, 1, 13, 13] 594 rigid atoms, others: [37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 794 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 27, 14, 14, 14, 14, 9, 9] 42 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758325 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758325/1 /scratch/stefan/7898178/working/building/REAL300019758325 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/252 `/scratch/stefan/7898178/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=NN=N[N-]1) `REAL300019758325.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [58, 38, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 13, 13, 6, 13, 13, 13, 1, 58, 91, 91, 91, 91, 58, 58, 58, 58, 38, 38, 18, 18, 18, 1, 1, 1, 6, 13, 13, 12, 13, 1, 1] 594 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 347 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [179, 155, 89, 38, 89, 13, 38, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 13, 179, 198, 198, 198, 198, 179, 179, 179, 179, 155, 155, 89, 89, 89, 13, 13, 13, 39, 1, 1, 1, 1, 13, 13] 594 rigid atoms, others: [37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 794 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758325 none CC(CN(C)C(=O)C1CC(O)(C2=CC=CC(Cl)=C2)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 27, 14, 14, 14, 14, 9, 9] 42 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758325 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758325 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758325/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758325/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758325 Building REAL300019758326 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758326' /scratch/stefan/7898178/working/building/REAL300019758326 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758326 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758326/0 /scratch/stefan/7898178/working/building/REAL300019758326 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/253 `/scratch/stefan/7898178/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=N[N-]N=N1) `REAL300019758326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758326 none CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 19, 6, 19, 1, 6, 1, 1, 1, 1, 8, 8, 15, 15, 27, 32, 32, 32, 1, 39, 61, 61, 61, 61, 39, 39, 39, 39, 28, 28, 19, 19, 19, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [51, 34, 35, 36, 5, 7, 8, 9, 10, 50, 19, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 301 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758326 none CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 22, 22, 39, 39, 58, 58, 58, 148, 148, 170, 170, 201, 201, 201, 201, 58, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 22, 22, 22, 58, 58, 58, 58, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58] 201 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 592 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758326 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758326/1 /scratch/stefan/7898178/working/building/REAL300019758326 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/254 `/scratch/stefan/7898178/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=NN=N[N-]1) `REAL300019758326.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758326 none CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 19, 6, 19, 1, 6, 1, 1, 1, 1, 8, 8, 15, 15, 27, 32, 32, 32, 1, 39, 62, 62, 62, 62, 39, 39, 39, 39, 28, 28, 19, 19, 19, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [51, 34, 35, 36, 5, 7, 8, 9, 10, 50, 19, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 301 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758326 none CC(CN(C)C(=O)C1CC(N(C)C(=O)OC(C)(C)C)C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 22, 22, 39, 39, 58, 58, 58, 148, 148, 170, 170, 201, 201, 201, 201, 58, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 22, 22, 22, 58, 58, 58, 58, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58] 201 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 592 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758326 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758326 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758326/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758326/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758326 Building REAL300019758327 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758327' /scratch/stefan/7898178/working/building/REAL300019758327 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758327 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758327/0 /scratch/stefan/7898178/working/building/REAL300019758327 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/255 `/scratch/stefan/7898178/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=NN=N[N-]1) `REAL300019758327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758327 none CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 46, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 46, 46, 17, 17, 17, 1, 1, 1, 1] 53 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758327 none CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 16, 26, 26, 46, 46, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 26, 26, 26, 53, 53, 53, 53] 53 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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]) total number of confs: 174 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758327 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758327/1 /scratch/stefan/7898178/working/building/REAL300019758327 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/256 `/scratch/stefan/7898178/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=N[N-]N=N1) `REAL300019758327.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758327 none CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 46, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 46, 46, 17, 17, 17, 1, 1, 1, 1] 53 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758327 none CC(CN(C)C(=O)C1=C2C=CC=CN2C(C(F)(F)F)=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 8, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 15, 25, 25, 46, 46, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 25, 25, 25, 53, 53, 53, 53] 53 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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]) total number of confs: 173 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758327 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758327 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758327/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758327/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758327 Building REAL300019758328 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758328' /scratch/stefan/7898178/working/building/REAL300019758328 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758328 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758328/0 /scratch/stefan/7898178/working/building/REAL300019758328 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/257 `/scratch/stefan/7898178/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=N[N-]N=N1) `REAL300019758328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758328 none CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 14, 5, 5, 11, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [81, 55, 28, 11, 28, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 81, 108, 108, 108, 108, 81, 81, 81, 81, 55, 55, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1] 143 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 17, 41] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 403 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758328 none CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 14, 5, 5, 11, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 13, 18, 18, 22, 22, 29, 29, 29, 29, 29, 32, 32, 32, 32, 29, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 18, 18, 18, 29, 29, 29, 32, 32, 32, 32, 32, 32, 29] 32 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758328 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758328/1 /scratch/stefan/7898178/working/building/REAL300019758328 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/258 `/scratch/stefan/7898178/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=NN=N[N-]1) `REAL300019758328.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758328 none CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 14, 5, 5, 11, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [82, 56, 29, 11, 29, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 82, 109, 109, 109, 109, 82, 82, 82, 82, 56, 56, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1] 145 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 17, 41] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 405 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758328 none CC(CN(C)C(=O)C1=CC=CC(N=S(C)(C)=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 14, 5, 5, 11, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 13, 18, 18, 22, 22, 29, 29, 29, 29, 29, 32, 32, 32, 32, 29, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 18, 18, 18, 29, 29, 29, 32, 32, 32, 32, 32, 32, 29] 32 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758328 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758328 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758328/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758328/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758328 Building REAL300019758329 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758329' /scratch/stefan/7898178/working/building/REAL300019758329 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758329 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758329/0 /scratch/stefan/7898178/working/building/REAL300019758329 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/259 `/scratch/stefan/7898178/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=N[N-]N=N1) `REAL300019758329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758329 none CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 46, 46, 46, 46, 37, 37, 37, 37, 32, 32, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 46 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758329 none CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 17, 26, 26, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758329 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758329/1 /scratch/stefan/7898178/working/building/REAL300019758329 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/260 `/scratch/stefan/7898178/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=NN=N[N-]1) `REAL300019758329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758329 none CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 46, 46, 46, 46, 37, 37, 37, 37, 32, 32, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 46 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758329 none CC(CN(C)C(=O)C1=CN2CC(C)CCC2=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 17, 26, 26, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758329 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758329 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758329/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758329/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758329 Building REAL300019758330 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758330' /scratch/stefan/7898178/working/building/REAL300019758330 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758330 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758330/0 /scratch/stefan/7898178/working/building/REAL300019758330 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/261 `/scratch/stefan/7898178/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=NN=N[N-]1) `REAL300019758330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 8 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 5, 5, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 5, 5, 5, 4, 3, 4, 4, 1, 1, 1, 1] 8 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 32 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758330 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758330/1 /scratch/stefan/7898178/working/building/REAL300019758330 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/262 `/scratch/stefan/7898178/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=N[N-]N=N1) `REAL300019758330.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 8 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 5, 5, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 5, 5, 5, 4, 3, 4, 4, 1, 1, 1, 1] 8 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758330 none CC(CN(C)C(=O)C1=CC=CC=C1C1=CC=NC=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40]) total number of confs: 32 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758330 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758330 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758330/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758330/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758330 Building REAL300019758331 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758331' /scratch/stefan/7898178/working/building/REAL300019758331 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758331 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758331/0 /scratch/stefan/7898178/working/building/REAL300019758331 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/263 `/scratch/stefan/7898178/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=N[N-]N=N1) `REAL300019758331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 113, 72, 34, 72, 6, 34, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 145, 201, 201, 201, 201, 145, 145, 145, 145, 113, 113, 72, 72, 72, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 741 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 122, 60, 122, 10, 60, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 122, 122, 122, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 804 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 27, 52, 52, 76, 76, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 27, 52, 52, 52, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 533 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758331 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758331/1 /scratch/stefan/7898178/working/building/REAL300019758331 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/264 `/scratch/stefan/7898178/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=NN=N[N-]1) `REAL300019758331.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 113, 72, 34, 72, 6, 34, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 144, 201, 201, 201, 201, 144, 144, 144, 144, 113, 113, 72, 72, 72, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 737 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 122, 60, 122, 10, 60, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 122, 122, 122, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 804 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758331 none CC(CN(C)C(=O)C=CC1=CC=CC(C2=CC=CC=C2)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 27, 51, 51, 75, 75, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 27, 51, 51, 51, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 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, 44, 45]) total number of confs: 531 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758331 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758331 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758331/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758331/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758331 Building REAL300019758332 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758332' /scratch/stefan/7898178/working/building/REAL300019758332 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758332 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758332/0 /scratch/stefan/7898178/working/building/REAL300019758332 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/265 `/scratch/stefan/7898178/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=NN=N[N-]1) `REAL300019758332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 21, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 39, 45, 45, 45, 45, 39, 39, 39, 39, 30, 30, 21, 21, 21, 1, 1, 6, 6, 6, 6, 6, 6, 1] 71 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 18, 41] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [66, 56, 45, 27, 45, 6, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 66, 71, 71, 71, 71, 66, 66, 66, 66, 56, 56, 45, 45, 45, 6, 6, 1, 1, 1, 1, 1, 1, 6] 71 rigid atoms, others: [35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 16, 25, 25, 34, 34, 44, 44, 44, 44, 44, 57, 57, 57, 57, 57, 44, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 25, 25, 25, 44, 44, 57, 57, 57, 57, 57, 57, 44] 57 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758332 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758332/1 /scratch/stefan/7898178/working/building/REAL300019758332 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/266 `/scratch/stefan/7898178/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=N[N-]N=N1) `REAL300019758332.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 21, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 39, 45, 45, 45, 45, 39, 39, 39, 39, 30, 30, 21, 21, 21, 1, 1, 6, 6, 6, 6, 6, 6, 1] 71 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 18, 41] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [66, 56, 45, 27, 45, 6, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 66, 71, 71, 71, 71, 66, 66, 66, 66, 56, 56, 45, 45, 45, 6, 6, 1, 1, 1, 1, 1, 1, 6] 71 rigid atoms, others: [35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758332 none CC(CN(C)C(=O)C1=CN=CC(N2CCCC2=O)=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 16, 25, 25, 34, 34, 44, 44, 44, 44, 44, 57, 57, 57, 57, 57, 44, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 25, 25, 25, 44, 44, 57, 57, 57, 57, 57, 57, 44] 57 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758332 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758332 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758332/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758332/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758332 Building REAL300019758333 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758333' /scratch/stefan/7898178/working/building/REAL300019758333 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758333 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758333/0 /scratch/stefan/7898178/working/building/REAL300019758333 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/267 `/scratch/stefan/7898178/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=NN=N[N-]1) `REAL300019758333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758333 none CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 11, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 137, 91, 31, 91, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 156, 156, 156, 156, 137, 137, 92, 92, 92, 6, 6, 1, 1, 2, 2, 1] 201 rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 712 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758333 none CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 11, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 23, 36, 36, 59, 59, 103, 187, 187, 187, 187, 187, 187, 187, 187, 1, 1, 1, 1, 1, 11, 11, 11, 11, 23, 23, 36, 36, 36, 103, 103, 187, 187, 187, 187, 187] 187 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758333 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758333/1 /scratch/stefan/7898178/working/building/REAL300019758333 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/268 `/scratch/stefan/7898178/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=N[N-]N=N1) `REAL300019758333.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758333 none CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 11, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 137, 91, 31, 91, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 156, 156, 156, 156, 137, 137, 92, 92, 92, 6, 6, 1, 1, 2, 2, 1] 201 rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 712 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758333 none CC(CN(C)C(=O)CC1=CC=C(C(N)=O)N=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.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, 5, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 11, 8, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 24, 36, 36, 58, 58, 102, 186, 186, 186, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 36, 36, 36, 102, 102, 186, 186, 186, 186, 186] 186 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 547 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758333 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758333 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758333/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758333/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758333 Building REAL300019758334 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758334' /scratch/stefan/7898178/working/building/REAL300019758334 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758334 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758334/0 /scratch/stefan/7898178/working/building/REAL300019758334 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/269 `/scratch/stefan/7898178/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=N[N-]N=N2)C1=O) `REAL300019758334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758334 none CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=N[N-]N=N2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 33, 33, 53, 53, 79, 87, 87, 109, 109, 109, 109, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 54, 54, 54, 79, 79, 87, 87, 87, 87] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758334 none CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=N[N-]N=N2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 106, 100, 81, 48, 81, 26, 48, 12, 1, 12, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109, 106, 106, 100, 100, 48, 48, 48, 26, 26, 12, 12, 12, 12] 109 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758334 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758334/1 /scratch/stefan/7898178/working/building/REAL300019758334 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/270 `/scratch/stefan/7898178/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=NN=N[N-]2)C1=O) `REAL300019758334.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758334 none CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=NN=N[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 33, 33, 53, 53, 78, 87, 87, 109, 109, 109, 109, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 54, 54, 54, 78, 78, 87, 87, 87, 87] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758334 none CC1=C(C)C(=O)N(CCC(=O)N(C)CC(C)C2=NN=N[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 11, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 105, 99, 78, 45, 78, 25, 45, 11, 1, 11, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109, 105, 105, 99, 99, 45, 45, 45, 25, 25, 11, 11, 11, 11] 109 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 426 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758334 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758334 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758334/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758334/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758334 Building REAL300019758335 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758335' /scratch/stefan/7898178/working/building/REAL300019758335 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758335 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758335/0 /scratch/stefan/7898178/working/building/REAL300019758335 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/271 `/scratch/stefan/7898178/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=N[N-]N=N1) `REAL300019758335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758335 none CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758335 none CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 19 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758335 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758335/1 /scratch/stefan/7898178/working/building/REAL300019758335 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/272 `/scratch/stefan/7898178/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=NN=N[N-]1) `REAL300019758335.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758335 none CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758335 none CC(CN(C)C(=O)C1CC2CSCC(C1)C2=O)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 1, 11, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 19 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758335 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758335 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758335/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758335/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758335 Building REAL300019758336 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758336' /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300019758336 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758336/0 /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/273 `/scratch/stefan/7898178/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C1) `REAL300019758336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 17, 19, 19, 22, 22, 22, 22, 1, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 17, 17, 19, 19, 19, 19, 1, 1] 65 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 47, 48, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=N[N-]N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 22, 65, 22, 22, 22, 22, 15, 10, 10, 10, 8, 10, 5, 1, 5, 1, 1, 1, 1, 1, 22, 65, 65, 65, 65, 65, 22, 22, 22, 22, 22, 22, 22, 15, 15, 10, 10, 10, 8, 8, 5, 5, 5, 5, 22, 22] 65 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758336/1 /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/274 `/scratch/stefan/7898178/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1) `REAL300019758336.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 17, 19, 19, 22, 22, 22, 22, 1, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 17, 17, 19, 19, 19, 19, 1, 1] 65 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 47, 48, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCCN(CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 22, 65, 22, 22, 22, 22, 15, 10, 10, 10, 8, 10, 5, 1, 5, 1, 1, 1, 1, 1, 22, 65, 65, 65, 65, 65, 22, 22, 22, 22, 22, 22, 22, 15, 15, 10, 10, 10, 8, 8, 5, 5, 5, 5, 22, 22] 65 rigid atoms, others: [16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `2' /scratch/stefan/7898178/working/building/REAL300019758336/2 /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 2 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/275 `/scratch/stefan/7898178/working/3D/275' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC[N@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1) `REAL300019758336.mol2' -> `2.mol2' `temp.mol2' -> `REAL300019758336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758336/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCC[N@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 13, 13, 18, 23, 23, 29, 29, 29, 29, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 18, 18, 23, 23, 23, 23, 1, 1] 57 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 48, 49, 35, 24, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCC[N@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 55, 55, 29, 55, 29, 29, 29, 29, 25, 29, 22, 22, 22, 19, 22, 10, 1, 10, 1, 1, 1, 1, 1, 29, 57, 57, 57, 57, 57, 29, 29, 29, 29, 29, 29, 29, 25, 25, 22, 22, 22, 19, 19, 10, 10, 10, 10, 29, 29] 57 rigid atoms, others: [17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `3' /scratch/stefan/7898178/working/building/REAL300019758336/3 /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 3 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/276 `/scratch/stefan/7898178/working/3D/276' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC[N@@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1) `REAL300019758336.mol2' -> `3.mol2' `temp.mol2' -> `REAL300019758336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758336/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCC[N@@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 13, 13, 18, 23, 23, 29, 29, 29, 29, 1, 19, 19, 19, 18, 18, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 18, 18, 23, 23, 23, 23, 1, 1] 58 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 48, 49, 35, 24, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758336 none CCOC(=O)C1CCC[N@@H+](CC(=O)N(C)CC(C)C2=NN=N[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 55, 55, 29, 55, 29, 29, 29, 29, 25, 29, 22, 22, 22, 19, 22, 10, 1, 10, 1, 1, 1, 1, 1, 29, 57, 57, 57, 57, 57, 29, 29, 29, 29, 29, 29, 29, 25, 25, 22, 22, 22, 19, 19, 10, 10, 10, 10, 29, 29] 57 rigid atoms, others: [17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758336 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758336 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 2: /scratch/stefan/7898178/working/building/REAL300019758336/2.* 3: /scratch/stefan/7898178/working/building/REAL300019758336/3.* 1: /scratch/stefan/7898178/working/building/REAL300019758336/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758336/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758336 Building REAL300019758337 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758337' /scratch/stefan/7898178/working/building/REAL300019758337 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758337 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758337/0 /scratch/stefan/7898178/working/building/REAL300019758337 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/277 `/scratch/stefan/7898178/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C(=O)N(C)CC(C)C1=N[N-]N=N1)N1C=CC=C1C=O) `REAL300019758337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758337 none CCC(C)C(C(=O)N(C)CC(C)C1=N[N-]N=N1)N1C=CC=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 7, 5, 7, 4, 5, 3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 4, 4, 3, 3, 3, 3, 9, 9, 9, 9] 9 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758337 none CCC(C)C(C(=O)N(C)CC(C)C1=N[N-]N=N1)N1C=CC=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 4, 1, 3, 4, 4, 9, 9, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 12, 12, 12, 12, 12, 12, 1, 1, 1, 4] 12 rigid atoms, others: [4, 43, 44, 45, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46]) total number of confs: 62 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758337 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758337/1 /scratch/stefan/7898178/working/building/REAL300019758337 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/278 `/scratch/stefan/7898178/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C(=O)N(C)CC(C)C1=NN=N[N-]1)N1C=CC=C1C=O) `REAL300019758337.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758337 none CCC(C)C(C(=O)N(C)CC(C)C1=NN=N[N-]1)N1C=CC=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 8, 6, 8, 5, 6, 3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 3, 3, 3, 3, 9, 9, 9, 9] 9 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758337 none CCC(C)C(C(=O)N(C)CC(C)C1=NN=N[N-]1)N1C=CC=C1C=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 4, 1, 3, 4, 4, 9, 9, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 12, 12, 12, 12, 12, 12, 1, 1, 1, 4] 12 rigid atoms, others: [4, 43, 44, 45, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46]) total number of confs: 62 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758337 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758337 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758337/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758337/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758337 Building REAL300019758338 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758338' /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300019758338 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758338/0 /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/279 `/scratch/stefan/7898178/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=N[N-]N=N1) `REAL300019758338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 13, 14, 14, 14, 14, 13, 13, 13, 13, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 26 rigid atoms, others: [51, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 50, 48, 49, 18, 19, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 21, 13, 7, 13, 3, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 26, 26, 26, 26, 25, 25, 25, 25, 21, 21, 13, 13, 13, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 26 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 6, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 11 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758338/1 /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/280 `/scratch/stefan/7898178/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=NN=N[N-]1) `REAL300019758338.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 13, 14, 14, 14, 14, 13, 13, 13, 13, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 26 rigid atoms, others: [51, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 50, 48, 49, 18, 19, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 21, 13, 7, 13, 3, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 26, 26, 26, 26, 25, 25, 25, 25, 21, 21, 13, 13, 13, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 26 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC([NH+]2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 6, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 11 rigid atoms, others: [1, 20, 21, 22, 23, 24] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `2' /scratch/stefan/7898178/working/building/REAL300019758338/2 /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 2 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/281 `/scratch/stefan/7898178/working/3D/281' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=N[N-]N=N1) `REAL300019758338.mol2' -> `2.mol2' `temp.mol2' -> `REAL300019758338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758338/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 13, 21, 21, 21, 21, 13, 13, 13, 13, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 32 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 50, 47, 48, 17, 18, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 24, 17, 11, 17, 8, 11, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 32, 32, 32, 32, 30, 30, 30, 30, 24, 24, 17, 17, 17, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 32 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10] 12 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `3' /scratch/stefan/7898178/working/building/REAL300019758338/3 /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 3 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/282 `/scratch/stefan/7898178/working/3D/282' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=NN=N[N-]1) `REAL300019758338.mol2' -> `3.mol2' `temp.mol2' -> `REAL300019758338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758338/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 13, 21, 21, 21, 21, 13, 13, 13, 13, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 32 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 50, 47, 48, 17, 18, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 24, 17, 11, 17, 8, 11, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 32, 32, 32, 32, 30, 30, 30, 30, 24, 24, 17, 17, 17, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 32 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758338 none CC(CN(C)C(=O)C1CCC(N2CCOCC2)CC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10] 12 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758338 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758338 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 2: /scratch/stefan/7898178/working/building/REAL300019758338/2.* 3: /scratch/stefan/7898178/working/building/REAL300019758338/3.* 1: /scratch/stefan/7898178/working/building/REAL300019758338/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758338/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758338 Building REAL300019758339 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758339' /scratch/stefan/7898178/working/building/REAL300019758339 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758339 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758339/0 /scratch/stefan/7898178/working/building/REAL300019758339 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/283 `/scratch/stefan/7898178/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1C(F)(F)F) `REAL300019758339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758339 none CC1=NNC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 23, 23, 27, 27, 27, 27, 1, 1, 2, 2, 2, 2, 2, 2, 1, 8, 8, 8, 20, 20, 23, 23, 23, 23] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758339 none CC1=NNC(C(=O)N(C)CC(C)C2=N[N-]N=N2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [27, 27, 27, 27, 23, 20, 23, 16, 20, 9, 1, 9, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 16, 16, 9, 9, 9, 9] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758339 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758339/1 /scratch/stefan/7898178/working/building/REAL300019758339 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/284 `/scratch/stefan/7898178/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1C(F)(F)F) `REAL300019758339.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758339 none CC1=NNC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 23, 23, 27, 27, 27, 27, 1, 1, 2, 2, 2, 2, 2, 2, 1, 8, 8, 8, 20, 20, 23, 23, 23, 23] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758339 none CC1=NNC(C(=O)N(C)CC(C)C2=NN=N[N-]2)=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [27, 27, 27, 27, 23, 20, 23, 16, 20, 9, 1, 9, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 16, 16, 9, 9, 9, 9] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758339 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758339 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758339/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758339/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758339 Building REAL300019758340 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758340' /scratch/stefan/7898178/working/building/REAL300019758340 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758340 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758340/0 /scratch/stefan/7898178/working/building/REAL300019758340 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/285 `/scratch/stefan/7898178/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=N[N-]N=N1) `REAL300019758340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758340 none CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 15, 1, 1, 11, 1, 1, 15, 1, 8, 8, 8, 8, 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, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [38, 34, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 6, 1, 1, 1, 38, 49, 49, 49, 49, 38, 38, 38, 38, 34, 34, 24, 24, 24, 1, 6, 1] 49 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758340 none CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 15, 1, 1, 11, 1, 1, 15, 1, 8, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 20, 27, 27, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 12, 12, 12, 12, 20, 20, 27, 27, 27, 50, 50, 50] 50 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 162 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758340 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758340/1 /scratch/stefan/7898178/working/building/REAL300019758340 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/286 `/scratch/stefan/7898178/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=NN=N[N-]1) `REAL300019758340.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758340 none CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 15, 1, 1, 11, 1, 1, 15, 1, 8, 8, 8, 8, 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, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [40, 34, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 6, 1, 1, 1, 40, 51, 51, 51, 51, 40, 40, 40, 40, 34, 34, 24, 24, 24, 1, 6, 1] 51 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758340 none CC(CN(C)C(=O)C1=CC(F)=C(C=O)C=C1F)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 15, 1, 1, 11, 1, 1, 15, 1, 8, 8, 8, 8, 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, 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 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 21, 28, 28, 38, 38, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 28, 28, 28, 52, 52, 52] 52 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 170 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758340 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758340 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758340/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758340/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758340 Building REAL300019758341 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758341' /scratch/stefan/7898178/working/building/REAL300019758341 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758341 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758341/0 /scratch/stefan/7898178/working/building/REAL300019758341 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/287 `/scratch/stefan/7898178/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1) `REAL300019758341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 3, 6, 1, 3, 1, 1, 1, 3, 3, 5, 10, 14, 14, 14, 14, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [37, 7, 8, 9, 45, 46, 19, 20, 21, 22, 5] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 16, 17, 14, 16, 14, 13, 12, 13, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 4, 4, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 42 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 4, 4, 6, 6, 6, 6, 7, 7, 9, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6] 15 rigid atoms, others: [1, 23, 24, 25, 26, 27] set([0, 2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758341 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758341/1 /scratch/stefan/7898178/working/building/REAL300019758341 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/288 `/scratch/stefan/7898178/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1) `REAL300019758341.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 3, 6, 1, 3, 1, 1, 1, 3, 3, 5, 10, 14, 14, 14, 14, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [37, 7, 8, 9, 45, 46, 19, 20, 21, 22, 5] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 16, 17, 14, 16, 14, 13, 12, 13, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 4, 4, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 42 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758341 none CC(CN(C)C(=O)C1N(C(=O)OCC2=CC=CC=C2)CC1(C)C)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 4, 4, 6, 6, 6, 6, 7, 7, 9, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6] 15 rigid atoms, others: [1, 23, 24, 25, 26, 27] set([0, 2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758341 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758341 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758341/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758341/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758341 Building REAL300019758342 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758342' /scratch/stefan/7898178/working/building/REAL300019758342 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758342 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758342/0 /scratch/stefan/7898178/working/building/REAL300019758342 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/289 `/scratch/stefan/7898178/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=N[N-]N=N1) `REAL300019758342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758342 none CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [23, 20, 8, 7, 8, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 28, 28, 28, 28, 23, 23, 23, 23, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 28 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 41, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758342 none CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [8, 1, 8, 12, 17, 17, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758342 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758342/1 /scratch/stefan/7898178/working/building/REAL300019758342 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/290 `/scratch/stefan/7898178/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=NN=N[N-]1) `REAL300019758342.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758342 none CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [23, 20, 8, 7, 8, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 28, 28, 28, 28, 23, 23, 23, 23, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 28 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 41, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758342 none CC(CN(C)C(=O)C1=CC=C2OCCN(C)C2=C1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [8, 1, 8, 12, 17, 17, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758342 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758342 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758342/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758342/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758342 Building REAL300019758343 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758343' /scratch/stefan/7898178/working/building/REAL300019758343 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758343 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758343/0 /scratch/stefan/7898178/working/building/REAL300019758343 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/291 `/scratch/stefan/7898178/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=N[N-]N=N1) `REAL300019758343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758343 none CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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: [36, 31, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 44, 44, 44, 44, 36, 36, 36, 36, 31, 31, 16, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 44 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758343 none CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 18, 28, 28, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 28, 28, 28, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758343 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758343/1 /scratch/stefan/7898178/working/building/REAL300019758343 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/292 `/scratch/stefan/7898178/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=NN=N[N-]1) `REAL300019758343.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758343 none CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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: [36, 31, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 44, 44, 44, 44, 36, 36, 36, 36, 31, 31, 16, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 44 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758343 none CC(CN(C)C(=O)C1=CN2CCC(C)CC2=N1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 18, 28, 28, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 28, 28, 28, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [1, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758343 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758343 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758343/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758343/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758343 Building REAL300019758344 mkdir: created directory `/scratch/stefan/7898178/working/building/REAL300019758344' /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178/working /scratch/stefan/7898178 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300019758344 mkdir: created directory `0' /scratch/stefan/7898178/working/building/REAL300019758344/0 /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/293 `/scratch/stefan/7898178/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=N[N-]N=N1) `REAL300019758344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300019758344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758344 none CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 19 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758344 none CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=N[N-]N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 37 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178/working /scratch/stefan/7898178 mkdir: created directory `1' /scratch/stefan/7898178/working/building/REAL300019758344/1 /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178/working /scratch/stefan/7898178 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7898178/working/3D/294 `/scratch/stefan/7898178/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=NN=N[N-]1) `REAL300019758344.mol2' -> `1.mol2' `temp.mol2' -> `REAL300019758344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7898178/working/building/REAL300019758344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758344 none CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 19 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300019758344 none CC(CN(C)C(=O)C(C)(C)C[NH+]1CCOCC1)C1=NN=N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [1, 18, 19, 20, 21, 22] set([0, 2, 3, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 37 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178/working /scratch/stefan/7898178 Finished preparing REAL300019758344 Recording results /scratch/stefan/7898178/working /scratch/stefan/7898178 Appending to /scratch/stefan/7898178/finished/xaaaafj_worked.* 1: /scratch/stefan/7898178/working/building/REAL300019758344/1.* 0: /scratch/stefan/7898178/working/building/REAL300019758344/0.* Removing working files in /scratch/stefan/7898178/working/building/REAL300019758344 /scratch/stefan/7898178 Compressing combined databse files /scratch/stefan/7898178/finished/xaaaafj_worked.db2.gz /scratch/stefan/7898178/finished/xaaaafj_worked.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7898178/finished) ======================================================= Finalizing... removed `/scratch/stefan/7898178/working/3D/295' removed directory: `/scratch/stefan/7898178/working/3D' rmdir: removing directory, `/scratch/stefan/7898178/working/building' rmdir: removing directory, `/scratch/stefan/7898178/working' ls: No match. ls: No match.